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FreeBSD Ports: Biology

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Software related to biology.

CheckM-1.0.18
Quality assessment tool for the microbial genomes
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXft-2.3.3, libXrender-0.9.10_2, libffi-3.3, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, png-1.6.37, py27-DendroPy-4.4.0, py27-backports_abc-0.5, py27-cycler-0.10.0, py27-futures-3.3.0, py27-pyparsing-2.4.7, py27-pytz-2020.1,1, py27-scipy-1.2.2_1, py27-setuptools-44.0.0, py27-singledispatch-3.4.0.3_1, py27-six-1.14.0, py27-tornado-5.1.1, py35-cython-0.29.15, py37-dateutil-2.8.1, py37-kiwisolver-1.1.0,1, py37-matplotlib-2.2.4_2, py37-pysam-0.16.0, py37-tkinter-3.7.8_6, py38-numpy-1.16.6,1, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3, tcl86-8.6.10, tk86-8.6.10_1, xorgproto-2020.1
Also listed in: Python

FastTree-2.1.10_4
Approximately-maximum-likelihood phylogenetic trees from alignments
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gcc9-9.3.0_1, gmp-6.2.0, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.1.0, s390x-binutils-2.33.1_3,1

GroopM-0.3.4_2
Metagenomic binning suite
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, hdf-szip-2.1.1, hdf5-1.10.6,1, indexinfo-0.3.1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXft-2.3.3, libXrender-0.9.10_2, libffi-3.3, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, lzo2-2.10_1, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, png-1.6.37, py27-backports_abc-0.5, py27-cycler-0.10.0, py27-futures-3.3.0, py27-numexpr-2.7.1, py27-pyparsing-2.4.7, py27-pytz-2020.1,1, py27-scipy-1.2.2_1, py27-setuptools-44.0.0, py27-singledispatch-3.4.0.3_1, py27-six-1.14.0, py27-tables-3.5.2_1, py27-tornado-5.1.1, py37-dateutil-2.8.1, py37-kiwisolver-1.1.0,1, py37-matplotlib-2.2.4_2, py37-tkinter-3.7.8_6, py38-numpy-1.16.6,1, python27-2.7.18_1, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3, tcl86-8.6.10, tk86-8.6.10_1, ucl-1.03_5, xorgproto-2020.1
Also listed in: Python

InsightToolkit-5.0.1_6
Insight Toolkit
Long description | Changes | Main Web Site
Maintained by: woodsb02@FreeBSD.org
Requires: ca_root_nss-3.55, cmake-3.17.3_1, curl-7.71.1, eigen-3.3.7, expat-2.2.8, fftw-2.1.5_22, gcc9-9.3.0_1, gdcm-3.0.7, gettext-runtime-0.21, gmp-6.2.0, googletest-1.10.0_1, hdf-szip-2.1.1, hdf5-1.10.6,1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.4, jsoncpp-1.9.3, lcms2-2.11_1, libarchive-3.4.3,1, libffi-3.3, liblz4-1.9.2_1,1, libnghttp2-1.41.0, libuv-1.38.1, lzo2-2.10_1, mpc-1.1.0_2, mpfr-4.1.0, ninja-1.10.0,2, openjpeg-2.3.1, pkgconf-1.7.3,1, png-1.6.37, python37-3.7.8_1, readline-8.0.4, rhash-1.3.9, s390x-binutils-2.33.1_3,1, tiff-4.1.0
Also listed in: Science

Jellyfish-2.2.10_9
Fast, memory-efficient counting of k-mers in DNA
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, ca_root_nss-3.55, curl-7.71.1, gettext-runtime-0.21, gettext-tools-0.21, gmake-4.3_2, htslib-1.10.2, indexinfo-0.3.1, libdeflate-1.6, libedit-3.1.20191231,1, libffi-3.3, libnghttp2-1.41.0, libtextstyle-0.21, libtool-2.4.6_1, libunwind-20200331, libyaml-0.2.5, m4-1.4.18_1,1, perl5-5.32.0, pkgconf-1.7.3,1, ruby-2.6.6_1,1, yaggo-1.5.9

abyss-2.2.4_1
Assembly By Short Sequences: parallel, paired-end sequence assembler
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, bash-5.0.18_2, boost-libs-1.72.0_2, gettext-runtime-0.21, ghc-8.8.4, gmake-4.3_2, gmp-6.2.0, hs-pandoc-2.9.2_2, icu-67.1,1, indexinfo-0.3.1, libedit-3.1.20191231,1, libffi-3.3, libiconv-1.16, m4-1.4.18_1,1, perl5-5.32.0, readline-8.0.4, sqlite3-3.32.3_2,1

afni-20.2.08
Advanced Functional Neuro Imaging
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: R-4.0.2, R-cran-Rcpp-1.0.5, R-cran-RcppEigen-0.3.3.7.0_1, R-cran-lme4-1.1.23_1, R-cran-minqa-1.2.4_5, R-cran-nloptr-1.2.2.2, R-cran-psych-1.2.1_12, R-cran-snow-0.4.3_3, R-cran-statmod-1.4.34, avahi-app-0.7_3, boehm-gc-8.0.4_1, boehm-gc-threaded-8.0.4_1, ca_root_nss-3.55, cairo-1.16.0,2, cups-2.3.3_1, curl-7.71.1, dbus-1.12.20, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, endian-1.1, expat-2.2.8, f2c-20060810_6, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.13.92_2,1, freeglut-3.0.0_2, freetype2-2.10.2, fribidi-0.19.7, gcc9-9.3.0_1, gdbm-1.18.1_1, gettext-runtime-0.21, gettext-tools-0.21, ghostscript9-agpl-base-9.52_6, glib-2.56.3_9,1, gmake-4.3_2, gmp-6.2.0, gnome_subr-1.0, gnutls-3.6.14, gobject-introspection-1.56.1_1,1, graphite2-1.3.14, gsl-2.6, guile2-2.2.7_1, harfbuzz-2.6.8, hdf-szip-2.1.1, hdf5-1.10.6,1, icu-67.1,1, indexinfo-0.3.1, jasper-2.0.16_1, jbig2dec-0.18, jbigkit-2.1_1, jpeg-turbo-2.0.4, libGLU-9.0.1, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXaw-1.0.13_3,2, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.3, libXi-1.7.10,1, libXmu-1.1.3,1, libXpm-3.5.13, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.102,1, libepoll-shim-0.0.20200602, libffi-3.3, libfontenc-1.1.4, libiconv-1.16, libidn-1.35, libidn2-2.3.0_1, libltdl-2.4.6, libnghttp2-1.41.0, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.16.0, libtextstyle-0.21, libunistring-0.9.10_1, libunwind-20200331, libxcb-1.13.1, libxml2-2.9.10, libxshmfence-1.3, m4-1.4.18_1,1, mesa-libs-19.0.8_2, metis-5.1.0_8, mkfontscale-1.2.1, mpc-1.1.0_2, mpeg_encode-1.5b, mpfr-4.1.0, netcdf-4.7.3, netcdf-fortran-4.5.2, netpbm-10.91.01, nettle-3.6, nlopt-2.6.2, open-motif-2.3.8_1, openblas-0.3.9_2,1, p11-kit-0.23.20_1, pango-1.42.4_4, pciids-20200624, pcre-8.44, pcre2-10.35, perl5-5.32.0, pixman-0.40.0, pkgconf-1.7.3,1, png-1.6.37, poppler-data-0.4.9_4, py27-setuptools-44.0.0, py38-numpy-1.16.6,1, python27-2.7.18_1, python37-3.7.8_1, python38-3.8.5, qhull5-1.0_3, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3, tcl86-8.6.10, tiff-4.1.0, tk86-8.6.10_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.18.0_4, xbitmaps-1.1.2, xorg-fonts-truetype-7.7_1, xorgproto-2020.1
Also listed in: Science, Graphics, Perl5, Python

artemis-17.0.1.11
DNA sequence viewer and annotation tool
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: alsa-lib-1.1.2_2, bash-5.0.18_2, dejavu-2.37_1, expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gettext-runtime-0.21, giflib-5.2.1, gmake-4.3_2, indexinfo-0.3.1, java-zoneinfo-2020.a, javavmwrapper-2.7.5, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_2, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, mkfontscale-1.2.1, openjdk8-8.265.01.1, readline-8.0.4, xorgproto-2020.1
Also listed in: Java

avida-2.12.4
Auto-adaptive genetic system designed for ALife research
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ca_root_nss-3.55, cmake-3.17.3_1, curl-7.71.1, expat-2.2.8, gettext-runtime-0.21, indexinfo-0.3.1, jsoncpp-1.9.3, libarchive-3.4.3,1, libffi-3.3, liblz4-1.9.2_1,1, libnghttp2-1.41.0, libuv-1.38.1, lzo2-2.10_1, ninja-1.10.0,2, python37-3.7.8_1, readline-8.0.4, rhash-1.3.9

babel-1.6_4
Converts among various molecular file formats
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Also listed in: Converters

bamtools-2.5.1_2
API and toolkit for handling BAM files
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: ca_root_nss-3.55, cmake-3.17.3_1, curl-7.71.1, expat-2.2.8, gettext-runtime-0.21, indexinfo-0.3.1, jsoncpp-1.9.3, libarchive-3.4.3,1, libffi-3.3, liblz4-1.9.2_1,1, libnghttp2-1.41.0, libuv-1.38.1, lzo2-2.10_1, ninja-1.10.0,2, python37-3.7.8_1, readline-8.0.4, rhash-1.3.9

bcftools-1.10.2
Tools for manipulating next-generation sequencing data
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, ca_root_nss-3.55, curl-7.71.1, gettext-runtime-0.21, gmake-4.3_2, gsl-2.6, htslib-1.10.2, indexinfo-0.3.1, libdeflate-1.6, libnghttp2-1.41.0, m4-1.4.18_1,1, perl5-5.32.0

bedtools-2.29.2
Toolset for genome set arithmetic such as intersect, union
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, libffi-3.3, python37-3.7.8_1, readline-8.0.4

bioawk-1.0.7
BWK awk modified for biological data
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

biococoa-2.2.2_6
Bioinformatics framework
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: avahi-app-0.7_3, ca_root_nss-3.55, cairo-1.16.0,2, cups-2.3.3_1, dbus-1.12.20, dbus-glib-0.110, expat-2.2.8, flac-1.3.3, flite-2.1, fontconfig-2.13.92_2,1, freetype2-2.10.2, gdbm-1.18.1_1, gettext-runtime-0.21, giflib-5.2.1, glib-2.56.3_9,1, gmake-4.3_2, gmp-6.2.0, gnome_subr-1.0, gnustep-back-0.27.0, gnustep-base-1.26.0_6, gnustep-gui-0.27.0_5, gnustep-make-2.7.0_3, gnutls-3.6.14, gobject-introspection-1.56.1_1,1, icu-67.1,1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.4, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.3, libXmu-1.1.3,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libao-1.2.0_5, libdaemon-0.14_1, libdrm-2.4.102,1, libepoll-shim-0.0.20200602, libffi-3.3, libgcrypt-1.8.5, libgpg-error-1.38, libiconv-1.16, libidn2-2.3.0_1, libobjc2-2.0_1, libogg-1.3.4,4, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libsndfile-1.0.29.p.20200620, libtasn1-4.16.0, libunistring-0.9.10_1, libunwind-20200331, libvorbis-1.3.7_2,3, libxcb-1.13.1, libxml2-2.9.10, libxshmfence-1.3, libxslt-1.1.34_1, mesa-libs-19.0.8_2, nettle-3.6, opus-1.3.1, p11-kit-0.23.20_1, pciids-20200624, pcre-8.44, pixman-0.40.0, png-1.6.37, python37-3.7.8_1, readline-8.0.4, tiff-4.1.0, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.18.0_4, xorgproto-2020.1
Also listed in: Gnustep

bolt-lmm-2.3.4_4
Mixed model association testing and variance component analysis
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: boehm-gc-8.0.4_1, boehm-gc-threaded-8.0.4_1, boost-libs-1.72.0_2, gcc9-9.3.0_1, gettext-runtime-0.21, gmake-4.3_2, gmp-6.2.0, guile2-2.2.7_1, icu-67.1,1, indexinfo-0.3.1, libffi-3.3, libltdl-2.4.6, libunistring-0.9.10_1, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, nlopt-2.6.2, openblas-0.3.9_2,1, py27-setuptools-44.0.0, py38-numpy-1.16.6,1, python27-2.7.18_1, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3

bowtie-1.1.2_9
Ultrafast, memory-efficient short read aligner
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmake-4.3_2, gmp-6.2.0, indexinfo-0.3.1, libffi-3.3, mpc-1.1.0_2, mpfr-4.1.0, perl5-5.32.0, python37-3.7.8_1, readline-8.0.4, s390x-binutils-2.33.1_3,1

bowtie2-2.4.1_2
Ultrafast, memory-efficient short read aligner
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: bash-5.0.18_2, gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, libffi-3.3, perl5-5.32.0, python37-3.7.8_1, readline-8.0.4, tbb-2020.3
Also listed in: Perl5, Python

bwa-0.7.17
Burrows-Wheeler sequence aligner
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, perl5-5.32.0

canu-2.0
Single molecule sequence assembler
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: ORBit2-2.14.19_2, adwaita-icon-theme-3.28.0, alsa-lib-1.1.2_2, argyllcms-1.9.2_5, at-spi2-atk-2.34.2, at-spi2-core-2.36.0, atk-2.36.0, avahi-app-0.7_3, boost-libs-1.72.0_2, brotli-1.0.7_2,1, ca_root_nss-3.55, cairo-1.16.0,2, colord-1.3.5, cups-2.3.3_1, dbus-1.12.20, dbus-glib-0.110, dconf-0.36.0, dejavu-2.37_1, enchant2-2.2.3_4, encodings-1.0.5,1, expat-2.2.8, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.13.92_2,1, freetype2-2.10.2, fribidi-0.19.7, gcc9-9.3.0_1, gconf2-3.2.6_5, gdbm-1.18.1_1, gdk-pixbuf2-2.40.0, geoclue-2.5.5, gettext-runtime-0.21, giflib-5.2.1, glib-2.56.3_9,1, glib-networking-2.56.1_2, gmake-4.3_2, gmp-6.2.0, gnome_subr-1.0, gnuplot-5.4.0, gnutls-3.6.14, gobject-introspection-1.56.1_1,1, graphene-1.10.0, graphite2-1.3.14, gsettings-desktop-schemas-3.28.1, gstreamer1-1.16.2, gstreamer1-plugins-1.16.2, gstreamer1-plugins-bad-1.16.2, gstreamer1-plugins-gl-1.16.2, gtk-update-icon-cache-3.24.20, gtk2-2.24.32, gtk3-3.24.20, harfbuzz-2.6.8, harfbuzz-icu-2.6.8_2, hicolor-icon-theme-0.17, hunspell-1.7.0_2, hyphen-2.8.8, icu-67.1,1, indexinfo-0.3.1, iso-codes-4.2, java-zoneinfo-2020.a, javavmwrapper-2.7.5, jbigkit-2.1_1, jpeg-turbo-2.0.4, json-glib-1.4.4, lcms2-2.11_1, libGLU-9.0.1, libICE-1.0.10,1, libIDL-0.8.14_4, libSM-1.2.3,1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.3, libXi-1.7.10,1, libXinerama-1.1.4_2,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libXxf86vm-1.1.4_3, libcroco-0.6.13, libdaemon-0.14_1, libdrm-2.4.102,1, libedit-3.1.20191231,1, libepoll-shim-0.0.20200602, libepoxy-1.5.4, libffi-3.3, libfontenc-1.1.4, libgcrypt-1.8.5, libgd-2.3.0,1, libgpg-error-1.38, libgsf-1.14.47_1, libiconv-1.16, libidn2-2.3.0_1, libinotify-20180201_2, libmspack-0.10.1, libnotify-0.7.8, libpaper-1.1.24.4, libpciaccess-0.16, libproxy-0.4.15, libpthread-stubs-0.4, librsvg2-2.40.21, libsecret-0.18.6_1, libsoup-2.62.3, libtasn1-4.16.0, libunistring-0.9.10_1, libunwind-20200331, libwpe-1.4.0.1, libxcb-1.13.1, libxkbcommon-0.10.0_2, libxml2-2.9.10, libxshmfence-1.3, libxslt-1.1.34_1, lua53-5.3.5_3, mesa-libs-19.0.8_2, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.1.0, nettle-3.6, nspr-4.27, openjdk8-8.265.01.1, openjpeg-2.3.1, orc-0.4.31, p11-kit-0.23.20_1, pango-1.42.4_4, pciids-20200624, pcre-8.44, perl5-5.32.0, pixman-0.40.0, png-1.6.37, polkit-0.116, py27-cairo-1.18.1_1, py27-gobject3-3.28.3_2, py27-setuptools-44.0.0, pygobject3-common-3.28.3_2, python27-2.7.18_1, python37-3.7.8_1, readline-8.0.4, s390x-binutils-2.33.1_3,1, shared-mime-info-1.10_2, spidermonkey60-60.9.0_4, sqlite3-3.32.3_2,1, tex-kpathsea-6.2.1_2, tiff-4.1.0, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.18.0_4, wayland-protocols-1.20, webkit2-gtk3-2.28.4, webp-1.1.0, woff2-1.0.2_4, wpebackend-fdo-1.4.1, wx30-gtk3-3.0.5.1, xkeyboard-config-2.30, xorg-fonts-truetype-7.7_1, xorgproto-2020.1
Also listed in: Java, Perl5

cd-hit-4.8.1_1
Clustering and comparing protein or nucleotide sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmake-4.3_2, gmp-6.2.0, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.1.0, s390x-binutils-2.33.1_3,1

cdbfasta-2010.07.22
Fast indexing and retrieval of FASTA records from flat file databases
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1

clustal-omega-1.2.4
Multiple alignment of nucleic acid and protein, replaces clustalw
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: argtable-2.13_2

clustalw-2.1_2
Multiple alignment program for DNA or proteins
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

cufflinks-2.2.1.89_1
Cufflinks assembles transcripts, estimates their abundance, etc
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, boost-libs-1.72.0_2, ca_root_nss-3.55, curl-7.71.1, eigen-3.3.7, gettext-runtime-0.21, gmake-4.3_2, htslib-1.10.2, icu-67.1,1, indexinfo-0.3.1, libdeflate-1.6, libffi-3.3, libnghttp2-1.41.0, m4-1.4.18_1,1, perl5-5.32.0, python37-3.7.8_1, readline-8.0.4

cytoscape-3.6.1
Software to visualize molecular interaction networks, gene expression
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: alsa-lib-1.1.2_2, bash-5.0.18_2, dejavu-2.37_1, expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gettext-runtime-0.21, giflib-5.2.1, indexinfo-0.3.1, java-zoneinfo-2020.a, javavmwrapper-2.7.5, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_2, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, maven-3.6.3, maven-wrapper-1_2, mkfontscale-1.2.1, openjdk8-8.265.01.1, readline-8.0.4, xorgproto-2020.1
Also listed in: Java

dDocent-2.7.8_1
Bash pipeline for RAD sequencing
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: ORBit2-2.14.19_2, adwaita-icon-theme-3.28.0, alsa-lib-1.1.2_2, argyllcms-1.9.2_5, at-spi2-atk-2.34.2, at-spi2-core-2.36.0, atk-2.36.0, avahi-app-0.7_3, bamtools-2.5.1_2, bash-5.0.18_2, bedtools-2.29.2, brotli-1.0.7_2,1, bwa-0.7.17, ca_root_nss-3.55, cairo-1.16.0,2, cd-hit-4.8.1_1, colord-1.3.5, coreutils-8.32, cups-2.3.3_1, curl-7.71.1, dbus-1.12.20, dbus-glib-0.110, dconf-0.36.0, dejavu-2.37_1, enchant2-2.2.3_4, encodings-1.0.5,1, expat-2.2.8, fastahack-1.0.0, fastp-0.20.1, filevercmp-g20151117, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.13.92_2,1, freebayes-1.2.0_2, freetype2-2.10.2, fribidi-0.19.7, fsom-g20151117_2, gawk-5.1.0, gcc9-9.3.0_1, gconf2-3.2.6_5, gdbm-1.18.1_1, gdk-pixbuf2-2.40.0, geoclue-2.5.5, gettext-runtime-0.21, giflib-5.2.1, glib-2.56.3_9,1, glib-networking-2.56.1_2, gmp-6.2.0, gnome_subr-1.0, gnuplot-5.4.0, gnutls-3.6.14, gobject-introspection-1.56.1_1,1, graphene-1.10.0, graphite2-1.3.14, gsettings-desktop-schemas-3.28.1, gstreamer1-1.16.2, gstreamer1-plugins-1.16.2, gstreamer1-plugins-bad-1.16.2, gstreamer1-plugins-gl-1.16.2, gtk-update-icon-cache-3.24.20, gtk2-2.24.32, gtk3-3.24.20, harfbuzz-2.6.8, harfbuzz-icu-2.6.8_2, hicolor-icon-theme-0.17, htslib-1.10.2, hunspell-1.7.0_2, hyphen-2.8.8, icu-67.1,1, indexinfo-0.3.1, intervaltree-g20151213_2, iso-codes-4.2, java-zoneinfo-2020.a, javavmwrapper-2.7.5, jbigkit-2.1_1, jpeg-turbo-2.0.4, json-glib-1.4.4, jsoncpp-1.9.3, lcms2-2.11_1, libGLU-9.0.1, libICE-1.0.10,1, libIDL-0.8.14_4, libSM-1.2.3,1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.3, libXi-1.7.10,1, libXinerama-1.1.4_2,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libXxf86vm-1.1.4_3, libcroco-0.6.13, libdaemon-0.14_1, libdeflate-1.6, libdrm-2.4.102,1, libedit-3.1.20191231,1, libepoll-shim-0.0.20200602, libepoxy-1.5.4, libffi-3.3, libfontenc-1.1.4, libgcrypt-1.8.5, libgd-2.3.0,1, libgpg-error-1.38, libgsf-1.14.47_1, libiconv-1.16, libidn2-2.3.0_1, libinotify-20180201_2, libmspack-0.10.1, libnghttp2-1.41.0, libnotify-0.7.8, libpaper-1.1.24.4, libpciaccess-0.16, libproxy-0.4.15, libpthread-stubs-0.4, librsvg2-2.40.21, libsecret-0.18.6_1, libsigsegv-2.12, libsoup-2.62.3, libtasn1-4.16.0, libunistring-0.9.10_1, libunwind-20200331, libwpe-1.4.0.1, libxcb-1.13.1, libxkbcommon-0.10.0_2, libxml2-2.9.10, libxshmfence-1.3, libxslt-1.1.34_1, lua53-5.3.5_3, mawk-1.3.4.20190203, mesa-libs-19.0.8_2, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.1.0, multichoose-1.0.3.2, nettle-3.6, nspr-4.27, openjdk8-8.265.01.1, openjpeg-2.3.1, orc-0.4.31, p11-kit-0.23.20_1, pango-1.42.4_4, parallel-20200722, pciids-20200624, pcre-8.44, pear-merger-0.9.6, perl5-5.32.0, pixman-0.40.0, png-1.6.37, polkit-0.116, py27-cairo-1.18.1_1, py27-gobject3-3.28.3_2, py27-setuptools-44.0.0, pygobject3-common-3.28.3_2, python27-2.7.18_1, python37-3.7.8_1, rainbow-2.0.4, readline-8.0.4, s390x-binutils-2.33.1_3,1, samtools-1.10, seqtk-1.2.8, shared-mime-info-1.10_2, smithwaterman-g20160702, spidermonkey60-60.9.0_4, sqlite3-3.32.3_2,1, stacks-2.4_1, tabixpp-1.0.0.10_1, tex-kpathsea-6.2.1_2, tiff-4.1.0, tpm-emulator-0.7.4_2, trimadap-0.1.3, trimmomatic-0.39, trousers-0.3.14_2, unzip-6.0_8, vcflib-1.0.0.r1.130_1, vcftools-0.1.16, wayland-1.18.0_4, wayland-protocols-1.20, webkit2-gtk3-2.28.4, webp-1.1.0, woff2-1.0.2_4, wpebackend-fdo-1.4.1, wx30-gtk3-3.0.5.1, xkeyboard-config-2.30, xorg-fonts-truetype-7.7_1, xorgproto-2020.1
Also listed in: Java, Perl5, Python

diamond-2.0.2
BLAST-compatible local sequence aligner
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: ca_root_nss-3.55, cmake-3.17.3_1, curl-7.71.1, expat-2.2.8, gettext-runtime-0.21, indexinfo-0.3.1, jsoncpp-1.9.3, libarchive-3.4.3,1, libffi-3.3, liblz4-1.9.2_1,1, libnghttp2-1.41.0, libuv-1.38.1, lzo2-2.10_1, ninja-1.10.0,2, python37-3.7.8_1, readline-8.0.4, rhash-1.3.9

dsr-pdb-1.0.3_5
Simple C++ PDB reader (reads the protein description format)
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: boost-libs-1.72.0_2, gettext-runtime-0.21, gmake-4.3_2, icu-67.1,1, indexinfo-0.3.1

emboss-6.6.0_4
Collection of open source tools for genetic sequence analysis
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: clustalw-2.1_2, expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gettext-runtime-0.21, giflib-5.2.1, gmake-4.3_2, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.4, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXaw-1.0.13_3,2, libXdmcp-1.1.3, libXext-1.3.4,1, libXft-2.3.3, libXmu-1.1.3,1, libXpm-3.5.13, libXrender-0.9.10_2, libXt-1.2.0,1, libgd-2.3.0,1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, open-motif-2.3.8_1, png-1.6.37, primer3-2.3.6, tiff-4.1.0, webp-1.1.0, xbitmaps-1.1.2, xorgproto-2020.1

exonerate-2.4.0
Generic tool for sequence alignment
Long description | Changes | Main Web Site
Maintained by: mzaki@niid.go.jp
Requires: gettext-runtime-0.21, glib-2.56.3_9,1, indexinfo-0.3.1, libffi-3.3, libiconv-1.16, libxml2-2.9.10, pcre-8.44, pkgconf-1.7.3,1, python37-3.7.8_1, readline-8.0.4

fasta-21.1.1
Collection of programs for searching DNA and protein databases
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

fasta3-36.3.8
Collection of programs for searching DNA and protein databases
Long description | Changes | Main Web Site
Maintained by: wendell@bsd.com.br

fastahack-1.0.0
Utility for indexing and sequence extraction from FASTA files
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

fastdnaml-1.2.2_2
Faster DNAML, makes phylogenetic trees using maximum likelihood
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

fastool-0.1.4
Simple and quick FastQ and FastA tool for file reading and conversion
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

fastp-0.20.1
Ultra-fast all-in-one FASTQ preprocessor
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1

fastqc-0.11.8
Quality control tool for high throughput sequence data
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: alsa-lib-1.1.2_2, dejavu-2.37_1, expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gettext-runtime-0.21, giflib-5.2.1, indexinfo-0.3.1, java-zoneinfo-2020.a, javavmwrapper-2.7.5, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_2, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, mkfontscale-1.2.1, openjdk8-8.265.01.1, perl5-5.32.0, xorgproto-2020.1
Also listed in: Java, Perl5

fastx_toolkit-0.0.14
CLI tools for Short-Reads FASTA/FASTQ files preprocessing
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, indexinfo-0.3.1, libgtextutils-0.7, libtool-2.4.6_1, m4-1.4.18_1,1, perl5-5.32.0, pkgconf-1.7.3,1

figtree-1.4.4
Graphical viewer of phylogenetic trees
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: alsa-lib-1.1.2_2, apache-ant-1.10.7, dejavu-2.37_1, expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gettext-runtime-0.21, giflib-5.2.1, indexinfo-0.3.1, java-zoneinfo-2020.a, javavmwrapper-2.7.5, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_2, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, mkfontscale-1.2.1, openjdk8-8.265.01.1, xorgproto-2020.1
Also listed in: Java

fluctuate-1.40
Program to fit population models
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

freebayes-1.2.0_2
Bayesian haplotype-based polymorphism discovery and genotyping
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1

garlic-1.6_1
Molecular viewer, editor, and visualization program
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, libX11-1.6.10_1,1, libXau-1.0.9, libXdmcp-1.1.3, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, xorgproto-2020.1

gatk-4.1.8.0
Variant discovery in high-throughput sequencing data
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: alsa-lib-1.1.2_2, dejavu-2.37_1, expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gettext-runtime-0.21, giflib-5.2.1, gradle62-6.2.2_1, indexinfo-0.3.1, java-zoneinfo-2020.a, javavmwrapper-2.7.5, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_2, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, mkfontscale-1.2.1, openjdk8-8.265.01.1, xorgproto-2020.1
Also listed in: Java

gcta-1.26.0_1
Genome-wide Complex Trait Analysis
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: eigen-3.3.7, gcc9-9.3.0_1, gettext-runtime-0.21, gmake-4.3_2, gmp-6.2.0, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, s390x-binutils-2.33.1_3,1

gemma-0.98.1_5
Genome-wide Efficient Mixed Model Association
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: eigen-3.3.7, gcc9-9.3.0_1, gettext-runtime-0.21, gmake-4.3_2, gmp-6.2.0, gsl-2.6, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, s390x-binutils-2.33.1_3,1

gff2ps-0.98l
Converts gff-formated genomic data-sets to PostScript
Long description | Changes | Main Web Site
Maintained by: egypcio@FreeBSD.org
Requires: bash-5.0.18_2, gawk-5.1.0, gettext-runtime-0.21, indexinfo-0.3.1, libsigsegv-2.12, readline-8.0.4

gmap-2015.09.21
Genomic Mapping and Alignment Program for mRNA and EST Sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, perl5-5.32.0

gperiodic-3.0.3
Displays a periodic table of the elements
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: atk-2.36.0, avahi-app-0.7_3, ca_root_nss-3.55, cairo-1.16.0,2, cups-2.3.3_1, dbus-1.12.20, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.8, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.13.92_2,1, freetype2-2.10.2, fribidi-0.19.7, gdbm-1.18.1_1, gdk-pixbuf2-2.40.0, gettext-runtime-0.21, gettext-tools-0.21, glib-2.56.3_9,1, gmp-6.2.0, gnome_subr-1.0, gnutls-3.6.14, gobject-introspection-1.56.1_1,1, graphite2-1.3.14, gtk-update-icon-cache-3.24.20, gtk2-2.24.32, harfbuzz-2.6.8, hicolor-icon-theme-0.17, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.4, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.3, libXi-1.7.10,1, libXinerama-1.1.4_2,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.102,1, libepoll-shim-0.0.20200602, libffi-3.3, libfontenc-1.1.4, libiconv-1.16, libidn2-2.3.0_1, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.16.0, libtextstyle-0.21, libunistring-0.9.10_1, libunwind-20200331, libxcb-1.13.1, libxml2-2.9.10, libxshmfence-1.3, mesa-libs-19.0.8_2, mkfontscale-1.2.1, nettle-3.6, p11-kit-0.23.20_1, pango-1.42.4_4, pciids-20200624, pcre-8.44, pixman-0.40.0, pkgconf-1.7.3,1, png-1.6.37, python37-3.7.8_1, readline-8.0.4, shared-mime-info-1.10_2, tiff-4.1.0, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.18.0_4, xorg-fonts-truetype-7.7_1, xorgproto-2020.1

graphlan-1.1.3
High-quality circular representations of taxonomic, phylogenetic trees
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.21, indexinfo-0.3.1, libffi-3.3, python27-2.7.18_1, readline-8.0.4

grappa-2.0
Genome Rearrangements Analysis and Phylogeny Software
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1

haplohseq-0.1.2_2
Identify regions of allelic imbalance
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: R-4.0.2, R-cran-getopt-1.20.3_1, R-cran-optparse-1.6.6, avahi-app-0.7_3, boost-libs-1.72.0_2, ca_root_nss-3.55, cairo-1.16.0,2, cups-2.3.3_1, curl-7.71.1, dbus-1.12.20, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.8, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.13.92_2,1, freetype2-2.10.2, fribidi-0.19.7, gcc9-9.3.0_1, gdbm-1.18.1_1, gettext-runtime-0.21, ghostscript9-agpl-base-9.52_6, glib-2.56.3_9,1, gmake-4.3_2, gmp-6.2.0, gnome_subr-1.0, gnutls-3.6.14, gobject-introspection-1.56.1_1,1, graphite2-1.3.14, harfbuzz-2.6.8, icu-67.1,1, indexinfo-0.3.1, jbig2dec-0.18, jbigkit-2.1_1, jpeg-turbo-2.0.4, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.3, libXmu-1.1.3,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.102,1, libepoll-shim-0.0.20200602, libffi-3.3, libfontenc-1.1.4, libiconv-1.16, libidn-1.35, libidn2-2.3.0_1, libnghttp2-1.41.0, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.16.0, libunistring-0.9.10_1, libunwind-20200331, libxcb-1.13.1, libxml2-2.9.10, libxshmfence-1.3, mesa-libs-19.0.8_2, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.1.0, nettle-3.6, p11-kit-0.23.20_1, pango-1.42.4_4, pciids-20200624, pcre-8.44, pcre2-10.35, pixman-0.40.0, png-1.6.37, poppler-data-0.4.9_4, python27-2.7.18_1, python37-3.7.8_1, readline-8.0.4, s390x-binutils-2.33.1_3,1, tcl86-8.6.10, tiff-4.1.0, tk86-8.6.10_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.18.0_4, xorg-fonts-truetype-7.7_1, xorgproto-2020.1

hhsuite-3.2.0_4
Remote protein homology detection suite
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: ca_root_nss-3.55, cmake-3.17.3_1, curl-7.71.1, expat-2.2.8, gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, hwloc-1.11.11, indexinfo-0.3.1, jsoncpp-1.9.3, libarchive-3.4.3,1, libevent-2.1.12, libffi-3.3, libltdl-2.4.6, liblz4-1.9.2_1,1, libnghttp2-1.41.0, libpciaccess-0.16, libuv-1.38.1, libxml2-2.9.10, lzo2-2.10_1, mpc-1.1.0_2, mpfr-4.1.0, munge-0.5.14_1, ninja-1.10.0,2, openmpi-4.0.4, pciids-20200624, perl5-5.32.0, python37-3.7.8_1, readline-8.0.4, rhash-1.3.9, s390x-binutils-2.33.1_3,1
Also listed in: Science

hisat2-2.1.0.23
Alignment program for mapping next-generation sequencing reads
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, libffi-3.3, perl5-5.32.0, python37-3.7.8_1, readline-8.0.4
Also listed in: Perl5, Python

hmmer-3.3
Profile hidden Markov models for biological sequence analysis
Long description | Changes | Main Web Site
Maintained by: mzaki@e-mail.ne.jp
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1

htslib-1.10.2
C library for high-throughput sequencing data formats
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, ca_root_nss-3.55, curl-7.71.1, gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, libdeflate-1.6, libnghttp2-1.41.0, m4-1.4.18_1,1, perl5-5.32.0
Also listed in: Devel

hyphy-2.5.15
Hypothesis testing using Phylogenies
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: ca_root_nss-3.55, cmake-3.17.3_1, curl-7.71.1, expat-2.2.8, gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, jsoncpp-1.9.3, libarchive-3.4.3,1, libffi-3.3, liblz4-1.9.2_1,1, libnghttp2-1.41.0, libuv-1.38.1, lzo2-2.10_1, mpc-1.1.0_2, mpfr-4.1.0, ninja-1.10.0,2, python37-3.7.8_1, readline-8.0.4, rhash-1.3.9, s390x-binutils-2.33.1_3,1

igv-2.5.3
Visualization tool for genomic datasets
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: adwaita-icon-theme-3.28.0, alsa-lib-1.1.2_2, aom-2.0.0_1, argp-standalone-1.3_4, argyllcms-1.9.2_5, at-spi2-atk-2.34.2, at-spi2-core-2.36.0, atk-2.36.0, avahi-app-0.7_3, ca_root_nss-3.55, cairo-1.16.0,2, colord-1.3.5, cups-2.3.3_1, dav1d-0.7.1, dbus-1.12.20, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.8, ffmpeg-4.3.1_1,1, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.13.92_2,1, freetype2-2.10.2, fribidi-0.19.7, gcc9-9.3.0_1, gdbm-1.18.1_1, gdk-pixbuf2-2.40.0, gettext-runtime-0.21, giflib-5.2.1, glib-2.56.3_9,1, gmp-6.2.0, gnome_subr-1.0, gnutls-3.6.14, gobject-introspection-1.56.1_1,1, gradle4-4.10.3, graphite2-1.3.14, gtk-update-icon-cache-3.24.20, gtk2-2.24.32, gtk3-3.24.20, harfbuzz-2.6.8, hicolor-icon-theme-0.17, icu-67.1,1, indexinfo-0.3.1, java-zoneinfo-2020.a, javavmwrapper-2.7.5, jbigkit-2.1_1, jpeg-turbo-2.0.4, lcms2-2.11_1, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.3, libXi-1.7.10,1, libXinerama-1.1.4_2,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libXxf86vm-1.1.4_3, libass-0.14.0, libcroco-0.6.13, libdaemon-0.14_1, libdrm-2.4.102,1, libedit-3.1.20191231,1, libepoll-shim-0.0.20200602, libepoxy-1.5.4, libffi-3.3, libfontenc-1.1.4, libgcrypt-1.8.5, libgpg-error-1.38, libgsf-1.14.47_1, libiconv-1.16, libidn2-2.3.0_1, libinotify-20180201_2, libogg-1.3.4,4, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, librsvg2-2.40.21, libtasn1-4.16.0, libtheora-1.1.1_7, libudev-devd-0.4.2, libunistring-0.9.10_1, libunwind-20200331, libv4l-1.18.0, libva-2.8.0, libvdpau-1.4, libvorbis-1.3.7_2,3, libvpx-1.9.0, libx264-0.160.3011, libxcb-1.13.1, libxkbcommon-0.10.0_2, libxml2-2.9.10, libxshmfence-1.3, libxslt-1.1.34_1, mesa-libs-19.0.8_2, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.1.0, nettle-3.6, nspr-4.27, opencv-core-3.4.1_35, openjdk8-8.265.01.1, openjfx8-devel-8.u202.b07_7,1, opus-1.3.1, p11-kit-0.23.20_1, pango-1.42.4_4, pciids-20200624, pcre-8.44, pixman-0.40.0, png-1.6.37, polkit-0.116, python37-3.7.8_1, readline-8.0.4, s390x-binutils-2.33.1_3,1, shared-mime-info-1.10_2, sndio-1.7.0, spidermonkey60-60.9.0_4, sqlite3-3.32.3_2,1, tiff-4.1.0, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.18.0_4, wayland-protocols-1.20, x265-3.2.1_4, xkeyboard-config-2.30, xorg-fonts-truetype-7.7_1, xorgproto-2020.1, xvid-1.3.7,1
Also listed in: Java

infernal-1.1.3
Search sequence databases for structural RNA homologs
Long description | Changes | Main Web Site
Maintained by: mzaki@e-mail.ne.jp
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1

io_lib-1.14.10
General purpose trace file (and Experiment File) reading interface
Long description | Changes | Main Web Site
Maintained by: danilo@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, ca_root_nss-3.55, curl-7.71.1, gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, libnghttp2-1.41.0, libtool-2.4.6_1, m4-1.4.18_1,1, perl5-5.32.0

iqtree-2.0.6
Efficient phylogenomic software by maximum likelihood
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: boost-libs-1.72.0_2, ca_root_nss-3.55, cmake-3.17.3_1, curl-7.71.1, eigen-3.3.7, expat-2.2.8, gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, icu-67.1,1, indexinfo-0.3.1, jsoncpp-1.9.3, libarchive-3.4.3,1, libffi-3.3, liblz4-1.9.2_1,1, libnghttp2-1.41.0, libuv-1.38.1, lzo2-2.10_1, mpc-1.1.0_2, mpfr-4.1.0, ninja-1.10.0,2, python37-3.7.8_1, readline-8.0.4, rhash-1.3.9, s390x-binutils-2.33.1_3,1

jalview-2.07_3
Viewer and editor for multiple sequence alignments
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: alsa-lib-1.1.2_2, apache-ant-1.10.7, dejavu-2.37_1, expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gettext-runtime-0.21, giflib-5.2.1, indexinfo-0.3.1, java-zoneinfo-2020.a, javavmwrapper-2.7.5, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_2, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, mkfontscale-1.2.1, openjdk8-8.265.01.1, xorgproto-2020.1
Also listed in: Java

kallisto-0.46.1
Quantify abundances of transcripts from RNA-Seq data
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, ca_root_nss-3.55, cmake-3.17.3_1, curl-7.71.1, expat-2.2.8, gettext-runtime-0.21, gmake-4.3_2, hdf-szip-2.1.1, hdf5-1.10.6,1, indexinfo-0.3.1, jsoncpp-1.9.3, libarchive-3.4.3,1, liblz4-1.9.2_1,1, libnghttp2-1.41.0, libuv-1.38.1, lzo2-2.10_1, m4-1.4.18_1,1, perl5-5.32.0, rhash-1.3.9

lagan-2.0_1
Efficient tools for large-scale multiple alignments of genomic DNA
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: perl5-5.32.0

lamarc-2.1.8_1
Package of programs for computing population parameters
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

libbigwig-0.4.4
C library for handling bigWig files (containing genomic data)
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: ca_root_nss-3.55, curl-7.71.1, gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, libnghttp2-1.41.0

libgtextutils-0.7
Gordon's text utilities
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, indexinfo-0.3.1, libtool-2.4.6_1, m4-1.4.18_1,1, perl5-5.32.0, pkgconf-1.7.3,1

libsbml-5.18.0
API Library for Working with SBML File
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: ca_root_nss-3.55, cmake-3.17.3_1, curl-7.71.1, expat-2.2.8, gettext-runtime-0.21, indexinfo-0.3.1, jsoncpp-1.9.3, libarchive-3.4.3,1, libffi-3.3, liblz4-1.9.2_1,1, libnghttp2-1.41.0, libuv-1.38.1, libxml2-2.9.10, lzo2-2.10_1, ninja-1.10.0,2, python37-3.7.8_1, readline-8.0.4, rhash-1.3.9
Also listed in: Devel

linux-foldingathome-7.6.13
Folding@home Client
Long description | Changes | Main Web Site
Maintained by: 0mp@FreeBSD.org
Requires: linux_base-c7-7.8.2003_1
Also listed in: Linux

mafft-7.266
Multiple alignment program for amino acid or nucleotide sequences
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1

mapm3-3.0
Constructs linkage maps of markers segregating in experimental crosses
Long description | Changes | Main Web Site
Maintained by: tphilipp@potion-studios.com

migrate-3.6.11
Program to estimate population sizes and migration rates
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

minc2-2.2.00_9
Medical Imaging NetCDF
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, bash-5.0.18_2, bison-3.6.4,1, ca_root_nss-3.55, curl-7.71.1, gettext-runtime-0.21, gmake-4.3_2, hdf-szip-2.1.1, hdf5-1.10.6,1, indexinfo-0.3.1, libnghttp2-1.41.0, libtextstyle-0.21, libtool-2.4.6_1, m4-1.4.18_1,1, netcdf-4.7.3, perl5-5.32.0, pkgconf-1.7.3,1, readline-8.0.4
Also listed in: Science

minimap2-2.17
Pairwise aligner for genomic and spliced nucleotide sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1

mmtf-cpp-1.0.0_2
C++ MMTF format API, decoder and encoder, for molecular structures
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: ca_root_nss-3.55, cmake-3.17.3_1, curl-7.71.1, expat-2.2.8, gettext-runtime-0.21, indexinfo-0.3.1, jsoncpp-1.9.3, libarchive-3.4.3,1, libffi-3.3, liblz4-1.9.2_1,1, libnghttp2-1.41.0, libuv-1.38.1, lzo2-2.10_1, msgpack-3.3.0, ninja-1.10.0,2, python37-3.7.8_1, readline-8.0.4, rhash-1.3.9
Also listed in: Science

molden-5.8.2_3
Display molecular orbitals and electron densities in 2D and 3D
Long description | Changes | Main Web Site
Maintained by: jmd@FreeBSD.org
Requires: expat-2.2.8, gcc9-9.3.0_1, gettext-runtime-0.21, gmake-4.3_2, gmp-6.2.0, indexinfo-0.3.1, libGLU-9.0.1, libX11-1.6.10_1,1, libXau-1.0.9, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXrandr-1.5.2, libXrender-0.9.10_2, libXxf86vm-1.1.4_3, libdrm-2.4.102,1, libepoll-shim-0.0.20200602, libffi-3.3, libpciaccess-0.16, libpthread-stubs-0.4, libunwind-20200331, libxcb-1.13.1, libxml2-2.9.10, libxshmfence-1.3, mesa-libs-19.0.8_2, mpc-1.1.0_2, mpfr-4.1.0, pciids-20200624, s390x-binutils-2.33.1_3,1, wayland-1.18.0_4, xorgproto-2020.1

mopac-7.1.15_8
Semi-empirical (MNDO, etc.) molecular orbital calculation
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmake-4.3_2, gmp-6.2.0, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.1.0, s390x-binutils-2.33.1_3,1

mothur-1.43.0
Software for bioinformatics of the microbial ecology community
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: bash-5.0.18_2, gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, readline-8.0.4

mrbayes-3.2.7_2
Bayesian inference of phylogeny
Long description | Changes | Main Web Site
Maintained by: mzaki@e-mail.ne.jp
Requires: indexinfo-0.3.1, readline-8.0.4

mummer-4.0.0.b2.2_2
Modular system for rapid whole genome alignment
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, libedit-3.1.20191231,1, libffi-3.3, libtool-2.4.6_1, libunwind-20200331, libyaml-0.2.5, m4-1.4.18_1,1, perl5-5.32.0, ruby-2.6.6_1,1, yaggo-1.5.9

muscle-3.8.1551
MUltiple Sequence Comparison by Log-Expectation
Long description | Changes | Main Web Site
Maintained by: mzaki@e-mail.ne.jp
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1

ncbi-blast-2.10.0_1
NCBI implementation of Basic Local Alignment Search Tool
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: ca_root_nss-3.55, gcc9-9.3.0_1, gettext-runtime-0.21, gmake-4.3_2, gmp-6.2.0, gnutls-3.6.14, indexinfo-0.3.1, libedit-3.1.20191231,1, libffi-3.3, libgcrypt-1.8.5, libgpg-error-1.38, libidn2-2.3.0_1, libnghttp2-1.41.0, libtasn1-4.16.0, libunistring-0.9.10_1, libuv-1.38.1, lmdb-0.9.24_2,1, lzo2-2.10_1, mpc-1.1.0_2, mpfr-4.1.0, nettle-3.6, p11-kit-0.23.20_1, p5-Exporter-Tiny-1.002002, p5-JSON-2.97.001, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, pcre-8.44, perl5-5.32.0, python37-3.7.8_1, readline-8.0.4, s390x-binutils-2.33.1_3,1, sqlite3-3.32.3_2,1, tpm-emulator-0.7.4_2, trousers-0.3.14_2
Also listed in: Perl5, Python

ncbi-cxx-toolkit-21.0.0_2
NCBI C++ Toolkit
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: bash-5.0.18_2, ca_root_nss-3.55, curl-7.71.1, cyrus-sasl-2.1.27_1, gettext-runtime-0.21, gmake-4.3_2, groff-1.22.4_3, indexinfo-0.3.1, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXpm-3.5.13, libXt-1.2.0,1, libedit-3.1.20191231,1, libevent-2.1.12, libffi-3.3, liblz4-1.9.2_1,1, libnghttp2-1.41.0, libpaper-1.1.24.4, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, mysql57-client-5.7.31, pcre-8.44, perl5-5.32.0, protobuf-3.12.3,1, psutils-1.17_5, python37-3.7.8_1, readline-8.0.4, uchardet-0.0.7, xorgproto-2020.1
Also listed in: Science, Devel

ncbi-toolkit-2017.01.06_5
NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: ca_root_nss-3.55, expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gettext-runtime-0.21, gmp-6.2.0, gnutls-3.6.14, indexinfo-0.3.1, jpeg-turbo-2.0.4, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXaw-1.0.13_3,2, libXdmcp-1.1.3, libXext-1.3.4,1, libXft-2.3.3, libXmu-1.1.3,1, libXpm-3.5.13, libXrender-0.9.10_2, libXt-1.2.0,1, libffi-3.3, libidn2-2.3.0_1, libpthread-stubs-0.4, libtasn1-4.16.0, libunistring-0.9.10_1, libxcb-1.13.1, libxml2-2.9.10, nettle-3.6, open-motif-2.3.8_1, p11-kit-0.23.20_1, png-1.6.37, tpm-emulator-0.7.4_2, trousers-0.3.14_2, xbitmaps-1.1.2, xorgproto-2020.1

nest-2.20.0_1
Simulator for spiking neural network models
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: ca_root_nss-3.55, cmake-3.17.3_1, curl-7.71.1, expat-2.2.8, gettext-runtime-0.21, gsl-2.6, indexinfo-0.3.1, jsoncpp-1.9.3, libarchive-3.4.3,1, libffi-3.3, libltdl-2.4.6, liblz4-1.9.2_1,1, libnghttp2-1.41.0, libuv-1.38.1, lzo2-2.10_1, ninja-1.10.0,2, pkgconf-1.7.3,1, py27-setuptools-44.0.0, py35-cython-0.29.15, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, readline-8.0.4, rhash-1.3.9
Also listed in: Science

ngs-sdk-2.10.5
Tools and libraries for using data in the INSDC Sequence Read Archives
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, perl5-5.32.0

p5-AcePerl-1.92_5
Perl5 interface to the ACEDB genome database system
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Cache-2.11, p5-Cache-Cache-1.08, p5-Digest-SHA1-2.13_1, p5-Error-0.17029, p5-File-NFSLock-1.29, p5-Heap-0.80_1, p5-IO-String-1.08_1, p5-IPC-ShareLite-0.17_1, p5-TimeDate-2.33,1, perl5-5.32.0
Also listed in: Databases, Perl5

p5-Bio-ASN1-EntrezGene-1.73_2
Regular expression-based Perl Parser for NCBI Entrez Gene
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: expat-2.2.8, libiconv-1.16, libxml2-2.9.10, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-Bio-Cluster-1.7.3_1, p5-Bio-Variation-1.7.5, p5-BioPerl-1.007007_1, p5-Class-Data-Inheritable-0.08_1, p5-Clone-0.45, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17029, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002002, p5-File-Listing-6.04_1, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.08, p5-HTTP-Daemon-6.12, p5-HTTP-Date-6.05, p5-HTTP-Message-6.25, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.068, p5-IO-String-1.08_1, p5-IO-Stringy-2.113, p5-IO-Tty-1.14, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4231, p5-Mozilla-CA-20200520, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.88, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.130, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-TimeDate-2.33,1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0205,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.30, p5-libwww-6.46, p5-libxml-0.08_1, perl5-5.32.0
Also listed in: Perl5

p5-Bio-Cluster-1.7.3_1
BioPerl cluster modules
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: expat-2.2.8, libiconv-1.16, libxml2-2.9.10, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-Bio-Variation-1.7.5, p5-BioPerl-1.007007_1, p5-Class-Data-Inheritable-0.08_1, p5-Clone-0.45, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17029, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002002, p5-File-Listing-6.04_1, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.08, p5-HTTP-Daemon-6.12, p5-HTTP-Date-6.05, p5-HTTP-Message-6.25, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.068, p5-IO-String-1.08_1, p5-IO-Stringy-2.113, p5-IO-Tty-1.14, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4231, p5-Mozilla-CA-20200520, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.88, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.130, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-TimeDate-2.33,1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0205,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.30, p5-libwww-6.46, p5-libxml-0.08_1, perl5-5.32.0
Also listed in: Perl5

p5-Bio-Coordinate-1.007001
Modules for working with biological coordinates
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: expat-2.2.8, libiconv-1.16, libxml2-2.9.10, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007007_1, p5-Class-Data-Inheritable-0.08_1, p5-Clone-0.45, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17029, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002002, p5-File-Listing-6.04_1, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.08, p5-HTTP-Daemon-6.12, p5-HTTP-Date-6.05, p5-HTTP-Message-6.25, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.068, p5-IO-String-1.08_1, p5-IO-Stringy-2.113, p5-IO-Tty-1.14, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4231, p5-Mozilla-CA-20200520, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.88, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.130, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-TimeDate-2.33,1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0205,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.30, p5-libwww-6.46, p5-libxml-0.08_1, perl5-5.32.0
Also listed in: Perl5

p5-Bio-DB-EMBL-1.7.4
Database object interface for EMBL entry retrieval
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: expat-2.2.8, libiconv-1.16, libxml2-2.9.10, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007007_1, p5-Class-Data-Inheritable-0.08_1, p5-Clone-0.45, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17029, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002002, p5-File-Listing-6.04_1, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.08, p5-HTTP-Daemon-6.12, p5-HTTP-Date-6.05, p5-HTTP-Message-6.25, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.068, p5-IO-String-1.08_1, p5-IO-Stringy-2.113, p5-IO-Tty-1.14, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4231, p5-Mozilla-CA-20200520, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.88, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.130, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-TimeDate-2.33,1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0205,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.30, p5-libwww-6.46, p5-libxml-0.08_1, perl5-5.32.0
Also listed in: Perl5

p5-Bio-DB-NCBIHelper-1.7.6
Collection of routines useful for queries to NCBI databases
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: expat-2.2.8, libiconv-1.16, libxml2-2.9.10, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-Bio-ASN1-EntrezGene-1.73_2,1, p5-Bio-Cluster-1.7.3_1, p5-Bio-Variation-1.7.5, p5-BioPerl-1.007007_1, p5-CGI-4.50, p5-Cache-2.11, p5-Cache-Cache-1.08, p5-Class-Data-Inheritable-0.08_1, p5-Clone-0.45, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Digest-SHA1-2.13_1, p5-Encode-Locale-1.05, p5-Error-0.17029, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002002, p5-File-Listing-6.04_1, p5-File-NFSLock-1.29, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.08, p5-HTTP-Daemon-6.12, p5-HTTP-Date-6.05, p5-HTTP-Message-6.25, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.068, p5-IO-String-1.08_1, p5-IO-Stringy-2.113, p5-IO-Tty-1.14, p5-IPC-Run-0.99, p5-IPC-ShareLite-0.17_1, p5-LWP-MediaTypes-6.04, p5-LWP-Protocol-https-6.09, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4231, p5-Mozilla-CA-20200520, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.88, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.130, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-TimeDate-2.33,1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0205,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.30, p5-libwww-6.46, p5-libxml-0.08_1, perl5-5.32.0
Also listed in: Perl5

p5-Bio-Das-1.17_4
Client-side library for Distributed Genome Annotation System
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: expat-2.2.8, libiconv-1.16, libxml2-2.9.10, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007007_1, p5-Class-Data-Inheritable-0.08_1, p5-Clone-0.45, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17029, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002002, p5-File-Listing-6.04_1, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.08, p5-HTTP-Daemon-6.12, p5-HTTP-Date-6.05, p5-HTTP-Message-6.25, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.068, p5-IO-String-1.08_1, p5-IO-Stringy-2.113, p5-IO-Tty-1.14, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4231, p5-Mozilla-CA-20200520, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.88, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.130, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-TimeDate-2.33,1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0205,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.30, p5-libwww-6.46, p5-libxml-0.08_1, perl5-5.32.0
Also listed in: Perl5

p5-Bio-Das-Lite-2.11_1
Perl extension for the DAS (HTTP+XML) Protocol
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: ca_root_nss-3.55, curl-7.71.1, libnghttp2-1.41.0, p5-Authen-NTLM-1.09_1, p5-Clone-0.45, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-File-Listing-6.04_1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTTP-Cookies-6.08, p5-HTTP-Daemon-6.12, p5-HTTP-Date-6.05, p5-HTTP-Message-6.25, p5-HTTP-Negotiate-6.01_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.068, p5-LWP-MediaTypes-6.04, p5-Module-Build-0.4231, p5-Mozilla-CA-20200520, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.88, p5-Readonly-2.05, p5-Socket6-0.29, p5-TimeDate-2.33,1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-Curl-4.17_4, p5-WWW-RobotRules-6.02_1, p5-libwww-6.46, perl5-5.32.0
Also listed in: Perl5

p5-Bio-FeatureIO-1.6.905
Handler for FeatureIO
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: expat-2.2.8, libiconv-1.16, libxml2-2.9.10, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007007_1, p5-Class-Data-Inheritable-0.08_1, p5-Clone-0.45, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17029, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002002, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.08, p5-HTTP-Daemon-6.12, p5-HTTP-Date-6.05, p5-HTTP-Message-6.25, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.068, p5-IO-String-1.08_1, p5-IO-Stringy-2.113, p5-IO-Tty-1.14, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4231, p5-Mozilla-CA-20200520, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.88, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.130, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-TimeDate-2.33,1, p5-Tree-DAG_Node-1.31, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0205,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.30, p5-libwww-6.46, p5-libxml-0.08_1, perl5-5.32.0
Also listed in: Perl5

p5-Bio-GFF3-2.0_2
Fast low-level functions for parsing and formatting GFF3
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Exporter-Tiny-1.002002, p5-File-ReadBackwards-1.05_1, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-URI-1.76, perl5-5.32.0
Also listed in: Perl5

p5-Bio-Glite-0.10_2
Perl Interface to G-language
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Authen-NTLM-1.09_1, p5-Clone-0.45, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-File-Listing-6.04_1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTTP-Cookies-6.08, p5-HTTP-Daemon-6.12, p5-HTTP-Date-6.05, p5-HTTP-Message-6.25, p5-HTTP-Negotiate-6.01_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.068, p5-LWP-MediaTypes-6.04, p5-Mozilla-CA-20200520, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.88, p5-Socket6-0.29, p5-TimeDate-2.33,1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-libwww-6.46, perl5-5.32.0
Also listed in: Perl5

p5-Bio-Graphics-2.40_2
Generate GD Images of Bio::Seq Objects
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: ca_root_nss-3.55, curl-7.71.1, expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gettext-runtime-0.21, giflib-5.2.1, indexinfo-0.3.1, io_lib-1.14.10, jbigkit-2.1_1, jpeg-turbo-2.0.4, libgd-2.3.0,1, libiconv-1.16, libnghttp2-1.41.0, libxml2-2.9.10, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-Bio-Coordinate-1.007001, p5-Bio-SCF-1.03_2, p5-BioPerl-1.007007_1, p5-CGI-4.50, p5-Class-Data-Inheritable-0.08_1, p5-Clone-0.45, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17029, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002002, p5-File-Listing-6.04_1, p5-GD-2.72, p5-GD-SVG-0.33_6, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.08, p5-HTTP-Daemon-6.12, p5-HTTP-Date-6.05, p5-HTTP-Message-6.25, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.068, p5-IO-String-1.08_1, p5-IO-Stringy-2.113, p5-IO-Tty-1.14, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4231, p5-Mozilla-CA-20200520, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.88, p5-SVG-2.85, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Statistics-Descriptive-3.0702, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.130, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-TimeDate-2.33,1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0205,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.30, p5-libwww-6.46, p5-libxml-0.08_1, perl5-5.32.0, png-1.6.37, tiff-4.1.0, webp-1.1.0
Also listed in: Perl5

p5-Bio-MAGETAB-1.31_2
Data model and utility API for the MAGE-TAB format
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Algorithm-C3-0.10_1, p5-B-Hooks-EndOfScope-0.24, p5-Carp-Clan-6.08, p5-Class-C3-0.34, p5-Class-Data-Inheritable-0.08_1, p5-Class-Inspector-1.36, p5-Class-Load-0.25, p5-Class-Load-XS-0.10, p5-Class-Method-Modifiers-2.13, p5-Class-Singleton-1.5_1, p5-Data-OptList-0.110, p5-Date-Manip-6.82, p5-DateTime-1.52, p5-DateTime-Format-DateManip-0.04_1, p5-DateTime-Locale-1.26, p5-DateTime-TimeZone-2.39,1, p5-Devel-GlobalDestruction-0.14, p5-Devel-OverloadInfo-0.005, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Dist-CheckConflicts-0.11_1, p5-Email-Valid-1.202, p5-Eval-Closure-0.14, p5-Exception-Class-1.44, p5-File-ShareDir-1.116, p5-MRO-Compat-0.13, p5-Mail-Tools-2.19, p5-Module-Implementation-0.09_1, p5-Module-Runtime-0.016, p5-Module-Runtime-Conflicts-0.003_1, p5-Moose-2.2013,1, p5-MooseX-FollowPBP-0.05_1, p5-MooseX-Types-0.50, p5-Net-DNS-1.25,1, p5-Net-Domain-TLD-1.74, p5-Package-DeprecationManager-0.17_1, p5-Package-Stash-0.38, p5-Package-Stash-XS-0.29, p5-Params-Coerce-0.14_2, p5-Params-Util-1.07_2, p5-Params-Validate-1.29, p5-Params-ValidationCompiler-0.30_1, p5-Parse-RecDescent-1.967015, p5-Role-Tiny-2.001004, p5-Scalar-List-Utils-1.55,1, p5-Specio-0.46, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-ForMethods-0.100052, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Identify-0.14, p5-Sub-Install-0.928_1, p5-Sub-Name-0.26,1, p5-Sub-Quote-2.006006, p5-Text-CSV_XS-1.34, p5-TimeDate-2.33,1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-Variable-Magic-0.62, p5-namespace-autoclean-0.29, p5-namespace-clean-0.27, perl5-5.32.0
Also listed in: Perl5

p5-Bio-NEXUS-0.78_1
Object-oriented Perl API for the NEXUS file format
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Clone-PP-1.07, perl5-5.32.0
Also listed in: Perl5

p5-Bio-Phylo-2.0.1
Phylogenetic analysis using Perl
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gettext-runtime-0.21, giflib-5.2.1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.4, libgd-2.3.0,1, libiconv-1.16, libxml2-2.9.10, p5-Algorithm-C3-0.10_1, p5-Algorithm-Combinatorics-0.27_1, p5-Algorithm-Diff-1.1903, p5-Archive-Zip-1.68, p5-Authen-NTLM-1.09_1, p5-B-Hooks-EndOfScope-0.24, p5-B-Hooks-OP-Check-0.22, p5-BioPerl-1.007007_1, p5-Cache-LRU-0.04_1, p5-Class-C3-0.34, p5-Class-Data-Inheritable-0.08_1, p5-Class-Inspector-1.36, p5-Class-Load-0.25, p5-Class-Load-XS-0.10, p5-Class-Method-Modifiers-2.13, p5-Class-Singleton-1.5_1, p5-Clone-0.45, p5-DBD-SQLite-1.64, p5-DBI-1.643, p5-DBIx-Connector-0.56, p5-Data-OptList-0.110, p5-Data-Perl-0.002011, p5-Data-Stag-0.14_2, p5-Data-TemporaryBag-0.09_1, p5-Data-UUID-1.226, p5-DateTime-1.52, p5-DateTime-Format-W3CDTF-0.07, p5-DateTime-Locale-1.26, p5-DateTime-TimeZone-2.39,1, p5-Devel-GlobalDestruction-0.14, p5-Devel-OverloadInfo-0.005, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Dist-CheckConflicts-0.11_1, p5-Encode-Locale-1.05, p5-Error-0.17029, p5-Eval-Closure-0.14, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002002, p5-File-Listing-6.04_1, p5-File-ShareDir-1.116, p5-Font-TTF-1.06, p5-GD-2.72, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.08, p5-HTTP-Daemon-6.12, p5-HTTP-Date-6.05, p5-HTTP-Message-6.25, p5-HTTP-Negotiate-6.01_1, p5-Hash-FieldHash-0.15, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.068, p5-IO-String-1.08_1, p5-IO-Stringy-2.113, p5-IO-Tty-1.14, p5-IPC-Run-0.99, p5-IRI-0.011, p5-JSON-2.97.001, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Log-Log4perl-1.50, p5-MRO-Compat-0.13, p5-Math-Bezier-Convert-0.02_1, p5-Math-CDF-0.1_2, p5-Math-Random-0.72, p5-Module-Build-0.4231, p5-Module-Implementation-0.09_1, p5-Module-Pluggable-5.2, p5-Module-Runtime-0.016, p5-Module-Runtime-Conflicts-0.003_1, p5-Moo-2.004000, p5-MooX-HandlesVia-0.001008, p5-Moose-2.2013,1, p5-MooseX-ArrayRef-0.005, p5-Mozilla-CA-20200520, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.88, p5-PDF-API2-2.037, p5-Package-DeprecationManager-0.17_1, p5-Package-Stash-0.38, p5-Package-Stash-XS-0.29, p5-Params-Util-1.07_2, p5-Params-Validate-1.29, p5-Params-ValidationCompiler-0.30_1, p5-Parse-RecDescent-1.967015, p5-RDF-Query-2.918, p5-RDF-Trine-1.019_1, p5-Ref-Util-XS-0.117, p5-Role-Tiny-2.001004, p5-SVG-2.85, p5-SWF-Builder-0.16_2, p5-SWF-File-0.42_2,1, p5-Scalar-List-Utils-1.55,1, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Specio-0.46, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Identify-0.14, p5-Sub-Install-0.928_1, p5-Sub-Name-0.26,1, p5-Sub-Quote-2.006006, p5-Sub-Uplevel-0.2800, p5-Term-ANSIColor-5.01, p5-Test-Deep-1.130, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Aligner-0.16, p5-Text-CSV_XS-1.34, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Text-Table-1.134, p5-Tie-IxHash-1.23_1, p5-TimeDate-2.33,1, p5-Try-Tiny-0.30, p5-Type-Tie-0.014, p5-Type-Tiny-1.010002, p5-Type-Tiny-XS-0.017, p5-URI-1.76, p5-Variable-Magic-0.62, p5-WWW-RobotRules-6.02_1, p5-XML-CommonNS-0.06_2, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0205,1, p5-XML-Namespace-0.02_1, p5-XML-NamespaceFactory-1.02, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XML2JSON-0.06_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.30, p5-YAML-Syck-1.32, p5-bareword-filehandles-0.007, p5-indirect-0.39, p5-libwww-6.46, p5-libxml-0.08_1, p5-multidimensional-0.014, p5-namespace-autoclean-0.29, p5-namespace-clean-0.27, p5-strictures-2.000006,1, perl5-5.32.0, png-1.6.37, tiff-4.1.0, webp-1.1.0
Also listed in: Perl5

p5-Bio-SCF-1.03_2
Read and Update SCF Chromatographic Sequence Files
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: ca_root_nss-3.55, curl-7.71.1, io_lib-1.14.10, libnghttp2-1.41.0, perl5-5.32.0
Also listed in: Perl5

p5-Bio-Variation-1.7.5
BioPerl variation-related functionality
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: expat-2.2.8, libiconv-1.16, libxml2-2.9.10, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007007_1, p5-Class-Data-Inheritable-0.08_1, p5-Clone-0.45, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17029, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002002, p5-File-Listing-6.04_1, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.08, p5-HTTP-Daemon-6.12, p5-HTTP-Date-6.05, p5-HTTP-Message-6.25, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.068, p5-IO-String-1.08_1, p5-IO-Stringy-2.113, p5-IO-Tty-1.14, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4231, p5-Mozilla-CA-20200520, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.88, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.130, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-TimeDate-2.33,1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0205,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.30, p5-libwww-6.46, p5-libxml-0.08_1, perl5-5.32.0
Also listed in: Perl5

p5-BioPerl-1.007007_1
Collection of Perl modules for bioinformatics
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: expat-2.2.8, libiconv-1.16, libxml2-2.9.10, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-Class-Data-Inheritable-0.08_1, p5-Clone-0.45, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17029, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002002, p5-File-Listing-6.04_1, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.08, p5-HTTP-Daemon-6.12, p5-HTTP-Date-6.05, p5-HTTP-Message-6.25, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.068, p5-IO-String-1.08_1, p5-IO-Stringy-2.113, p5-IO-Tty-1.14, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4231, p5-Mozilla-CA-20200520, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.88, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.130, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-TimeDate-2.33,1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0205,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.30, p5-libwww-6.46, p5-libxml-0.08_1, perl5-5.32.0
Also listed in: Perl5

p5-BioPerl-Run-1.007003
Wrapper modules for common bioinformatics tools
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: expat-2.2.8, libiconv-1.16, libxml2-2.9.10, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-Bio-Cluster-1.7.3_1, p5-Bio-FeatureIO-1.6.905, p5-Bio-Variation-1.7.5, p5-BioPerl-1.007007_1, p5-Class-Data-Inheritable-0.08_1, p5-Clone-0.45, p5-Config-Any-0.32, p5-Config-General-2.63, p5-Config-Tiny-2.24, p5-Cpanel-JSON-XS-4.19, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17029, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002002, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-File-Sort-1.01_1, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.08, p5-HTTP-Daemon-6.12, p5-HTTP-Date-6.05, p5-HTTP-Message-6.25, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.068, p5-IO-String-1.08_1, p5-IO-Stringy-2.113, p5-IO-Tty-1.14, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4231, p5-Module-Pluggable-5.2, p5-Mozilla-CA-20200520, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.88, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.130, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-TimeDate-2.33,1, p5-Tree-DAG_Node-1.31, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0205,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.57, p5-XML-Simple-2.25, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.30, p5-YAML-LibYAML-0.82, p5-libwww-6.46, p5-libxml-0.08_1, perl5-5.32.0
Also listed in: Perl5

p5-TrimGalore-0.6.5
Wrapper around Cutadapt and FastQC for adapter and quality trimming
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: alsa-lib-1.1.2_2, dejavu-2.37_1, expat-2.2.8, fastqc-0.11.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gettext-runtime-0.21, giflib-5.2.1, indexinfo-0.3.1, java-zoneinfo-2020.a, javavmwrapper-2.7.5, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libffi-3.3, libfontenc-1.1.4, libinotify-20180201_2, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, mkfontscale-1.2.1, openjdk8-8.265.01.1, perl5-5.32.0, pigz-2.4, py27-setuptools-44.0.0, py37-bz2file-0.98, py37-cutadapt-2.7, py37-dnaio-0.4.2, py37-xopen-0.8.4, python27-2.7.18_1, python37-3.7.8_1, readline-8.0.4, xorgproto-2020.1, zopfli-1.0.3_1
Also listed in: Perl5, Python

p5-transdecoder-5.4.0_2
Identify candidate coding regions within transcript sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: cd-hit-4.8.1_1, gcc9-9.3.0_1, gmp-6.2.0, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.1.0, p5-URI-1.76, perl5-5.32.0, s390x-binutils-2.33.1_3,1
Also listed in: Perl5

paml-4.9j
Phylogenetic Analysis by Maximum Likelihood (PAML)
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1

pbbam-0.18.0_5
PacBio BAM C++ library, with SWIG bindings
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: boost-libs-1.72.0_2, ca_root_nss-3.55, curl-7.71.1, gettext-runtime-0.21, htslib-1.10.2, icu-67.1,1, indexinfo-0.3.1, libdeflate-1.6, libffi-3.3, libnghttp2-1.41.0, meson-0.54.3, ninja-1.10.0,2, pkgconf-1.7.3,1, py27-setuptools-44.0.0, python27-2.7.18_1, python37-3.7.8_1, readline-8.0.4

pbcopper-0.4.1_4
Core C++ library for Pacific Biosciences tools
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: boost-libs-1.72.0_2, gettext-runtime-0.21, icu-67.1,1, indexinfo-0.3.1, libffi-3.3, meson-0.54.3, ninja-1.10.0,2, py27-setuptools-44.0.0, python27-2.7.18_1, python37-3.7.8_1, readline-8.0.4

pbseqan-g20171011
Pacific Biosciences patched and stripped down SeqAn
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

pear-merger-0.9.6
Memory-efficient and highly accurate paired-end read merger
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

phrap-1.090518
Program for assembling shotgun DNA sequence data
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp

phred-0.020425.c
Base calling and quality value assignment on DNA sequencing
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp

phylip-3.697
Phylogeny Inference Package
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: bash-5.0.18_2, gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXaw-1.0.13_3,2, libXdmcp-1.1.3, libXext-1.3.4,1, libXmu-1.1.3,1, libXpm-3.5.13, libXt-1.2.0,1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, readline-8.0.4, xorgproto-2020.1

phyml-3.3.20200621
Simple, fast, and accurate algorithm to estimate large phylogenies
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, indexinfo-0.3.1, libtool-2.4.6_1, m4-1.4.18_1,1, perl5-5.32.0, pkgconf-1.7.3,1

picard-tools-2.22.9
CLI tools for manipulating high-throughput sequencing (HTS) data
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: alsa-lib-1.1.2_2, ca_root_nss-3.55, curl-7.71.1, dejavu-2.37_1, expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gettext-runtime-0.21, giflib-5.2.1, htslib-1.10.2, indexinfo-0.3.1, java-zoneinfo-2020.a, javavmwrapper-2.7.5, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libdeflate-1.6, libfontenc-1.1.4, libinotify-20180201_2, libnghttp2-1.41.0, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, mkfontscale-1.2.1, openjdk8-8.265.01.1, samtools-1.10, xorgproto-2020.1
Also listed in: Java

plink-1.90.b6.17_1
Whole genome association analysis toolset
Long description | Changes | Main Web Site
Maintained by: mzaki@e-mail.ne.jp
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmake-4.3_2, gmp-6.2.0, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, s390x-binutils-2.33.1_3,1

primer3-2.3.6
Primer3 helps to choose primers for PCR reactions
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1

prodigal-2.6.3.7
Protein-coding gene prediction for prokaryotic genomes
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1

prodigy-lig-1.0.0.3_1
Prediction of protein-small molecule binding affinities
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: adobe-cmaps-20051217_4, expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gcc9-9.3.0_1, gettext-runtime-0.21, giflib-5.2.1, gmake-4.3_2, gmp-6.2.0, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.4, lcms2-2.11_1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXft-2.3.3, libXrender-0.9.10_2, libffi-3.3, libfontenc-1.1.4, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, metis-5.1.0_8, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, openjpeg-2.3.1, png-1.6.37, py27-olefile-0.46, py27-setuptools-44.0.0, py37-biopython-1.77, py37-pillow-7.0.0, py37-reportlab-3.5.21_1, py37-tkinter-3.7.8_6, py38-numpy-1.16.6,1, python27-2.7.18_1, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3, tcl86-8.6.10, tiff-4.1.0, tk86-8.6.10_1, webp-1.1.0, xorgproto-2020.1
Also listed in: Python

protomol-2.0.3_14
OO, component based, framework for molecular dynamics (MD) simulations
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: expat-2.2.8, freeglut-3.0.0_2, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.4, libGLU-9.0.1, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXmu-1.1.3,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libdrm-2.4.102,1, libepoll-shim-0.0.20200602, libffi-3.3, libpciaccess-0.16, libpthread-stubs-0.4, libunwind-20200331, libxcb-1.13.1, libxml2-2.9.10, libxshmfence-1.3, mesa-libs-19.0.8_2, pciids-20200624, png-1.6.37, tiff-4.1.0, wayland-1.18.0_4, xorgproto-2020.1

psi88-1.0_16
Plotting wavefunctions (molecular orbitals) in 3D
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gcc9-9.3.0_1, gmp-6.2.0, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.1.0, s390x-binutils-2.33.1_3,1

py27-Genesis-PyAPI-1.2.1
API for the Genesis platform for genetics information processing
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.21, indexinfo-0.3.1, libffi-3.3, py27-asn1crypto-1.3.0, py27-idna-2.8, py27-openssl-19.0.0, py27-pysocks-1.7.1, py27-requests-2.22.0, py27-setuptools-44.0.0, py27-six-1.14.0, py27-slumber-0.7.1, py37-certifi-2020.6.20, py37-cffi-1.14.1, py37-chardet-3.0.4_3, py37-cryptography-2.6.1, py37-pycparser-2.20, py37-urllib3-1.25.7,1, python27-2.7.18_1, python37-3.7.8_1, readline-8.0.4
Also listed in: Python

py27-biom-format-2.1.7_3
Biological Observation Matrix (BIOM) Format Project
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, hdf-szip-2.1.1, hdf5-1.10.6,1, indexinfo-0.3.1, libedit-3.1.20191231,1, libffi-3.3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, postgresql11-client-11.8, py27-future-0.18.2, py27-h5py-2.10.0, py27-numexpr-2.7.1, py27-pyqi-0.3.2_2, py27-pytz-2020.1,1, py27-scipy-1.2.2_1, py27-setuptools-44.0.0, py27-six-1.14.0, py35-sqlite3-3.5.9_7, py37-bottleneck-1.3.2, py37-click-7.0, py37-dateutil-2.8.1, py37-pandas-0.24.2_1,1, py38-numpy-1.16.6,1, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, sqlite3-3.32.3_2,1, suitesparse-5.8.1, tbb-2020.3
Also listed in: Python

py27-bx-python-0.8.9
Python module for reading, manipulating and writing genomic data sets
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, libffi-3.3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, py27-setuptools-44.0.0, py27-six-1.14.0, py35-cython-0.29.15, py38-numpy-1.16.6,1, python27-2.7.18_1, python35-3.5.9_6, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3
Also listed in: Python

py27-ete3-3.1.1
Framework for the analysis and visualization of trees
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: avahi-app-0.7_3, ca_root_nss-3.55, cups-2.3.3_1, dbus-1.12.20, dbus-glib-0.110, double-conversion-3.1.5.19, etc_os-release-0.1_3, expat-2.2.8, fontconfig-2.13.92_2,1, freeglut-3.0.0_2, freetype2-2.10.2, gcc9-9.3.0_1, gdbm-1.18.1_1, gettext-runtime-0.21, giflib-5.2.1, glib-2.56.3_9,1, gmp-6.2.0, gnome_subr-1.0, gnutls-3.6.14, gobject-introspection-1.56.1_1,1, graphite2-1.3.14, harfbuzz-2.6.8, hicolor-icon-theme-0.17, icu-67.1,1, indexinfo-0.3.1, jasper-2.0.16_1, jbigkit-2.1_1, jpeg-turbo-2.0.4, lcms-1.19_6,1, libGLU-9.0.1, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXmu-1.1.3,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.102,1, libepoll-shim-0.0.20200602, libevdev-1.5.9_1, libffi-3.3, libgcrypt-1.8.5, libgpg-error-1.38, libgudev-230_1, libiconv-1.16, libidn2-2.3.0_1, libinput-1.15.6, liblz4-1.9.2_1,1, libmng-1.0.10_3, libmtdev-1.1.5_2, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.16.0, libudev-devd-0.4.2, libunistring-0.9.10_1, libunwind-20200331, libwacom-1.4.1, libxcb-1.13.1, libxkbcommon-0.10.0_2, libxml2-2.9.10, libxshmfence-1.3, libxslt-1.1.34_1, mesa-libs-19.0.8_2, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, nettle-3.6, openblas-0.3.9_2,1, p11-kit-0.23.20_1, pciids-20200624, pcre-8.44, pcre2-10.35, png-1.6.37, py27-enum34-1.1.6, py27-evdev-0.8.1_1, py27-pyudev-0.22.0, py27-qt5-core-5.13.1_1, py27-qt5-gui-5.13.1_1, py27-qt5-opengl-5.13.1_1, py27-qt5-svg-5.13.1_1, py27-qt5-widgets-5.13.1_1, py27-setuptools-44.0.0, py27-sip-4.19.21,1, py27-six-1.14.0, py37-lxml-4.5.2, py37-qt5-printsupport-5.13.1_1, py38-numpy-1.16.6,1, python27-2.7.18_1, python37-3.7.8_1, python38-3.8.5, qscintilla2-qt5-2.11.4, qt5-core-5.15.0_2, qt5-dbus-5.15.0, qt5-gui-5.15.0, qt5-imageformats-5.15.0, qt5-network-5.15.0, qt5-opengl-5.15.0, qt5-printsupport-5.15.0, qt5-svg-5.15.0, qt5-widgets-5.15.0, qtchooser-66_3, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3, tiff-4.1.0, tpm-emulator-0.7.4_2, trousers-0.3.14_2, vulkan-headers-1.2.135.0, wayland-1.18.0_4, webp-1.1.0, xcb-util-0.4.0_2,1, xcb-util-image-0.4.0_1, xcb-util-keysyms-0.4.0_1, xcb-util-renderutil-0.3.9_1, xcb-util-wm-0.4.1_3, xdg-utils-1.1.3_1, xkeyboard-config-2.30, xorgproto-2020.1, xprop-1.2.4, xset-1.2.4_3, zstd-1.4.5
Also listed in: Python

py27-gtfparse-1.2.1
Parsing tools for GTF (gene transfer format) files
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Maintained by: yuri@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, libedit-3.1.20191231,1, libffi-3.3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, py27-numexpr-2.7.1, py27-pytz-2020.1,1, py27-setuptools-44.0.0, py27-six-1.14.0, py35-sqlite3-3.5.9_7, py37-bottleneck-1.3.2, py37-dateutil-2.8.1, py37-pandas-0.24.2_1,1, py38-numpy-1.16.6,1, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, sqlite3-3.32.3_2,1, suitesparse-5.8.1, tbb-2020.3
Also listed in: Python

py27-multiqc-1.8
Aggregate bioinformatics analysis reports across samples and tools
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Maintained by: jwb@FreeBSD.org
Requires: cairo-1.16.0,2, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.8, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.13.92_2,1, freetype2-2.10.2, fribidi-0.19.7, gcc9-9.3.0_1, gettext-runtime-0.21, giflib-5.2.1, glib-2.56.3_9,1, gmp-6.2.0, graphite2-1.3.14, graphviz-2.44.1, harfbuzz-2.6.8, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.4, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXaw-1.0.13_3,2, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.3, libXmu-1.1.3,1, libXpm-3.5.13, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libdrm-2.4.102,1, libepoll-shim-0.0.20200602, libffi-3.3, libfontenc-1.1.4, libgd-2.3.0,1, libiconv-1.16, libltdl-2.4.6, libpciaccess-0.16, libpthread-stubs-0.4, libunwind-20200331, libxcb-1.13.1, libxml2-2.9.10, libxshmfence-1.3, mesa-libs-19.0.8_2, metis-5.1.0_8, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, pango-1.42.4_4, pciids-20200624, pcre-8.44, pixman-0.40.0, png-1.6.37, py27-Babel-2.8.0, py27-Jinja2-2.10.1, py27-MarkupSafe-1.1.1, py27-asn1crypto-1.3.0, py27-backports_abc-0.5, py27-cycler-0.10.0, py27-future-0.18.2, py27-futures-3.3.0, py27-humanfriendly-7.1.1, py27-idna-2.8, py27-monotonic-1.5, py27-networkx-2.1,1, py27-openssl-19.0.0, py27-pygraphviz-1.5, py27-pyparsing-2.4.7, py27-pysocks-1.7.1, py27-pytz-2020.1,1, py27-requests-2.22.0, py27-scipy-1.2.2_1, py27-setuptools-44.0.0, py27-singledispatch-3.4.0.3_1, py27-six-1.14.0, py27-tornado-5.1.1, py37-certifi-2020.6.20, py37-cffi-1.14.1, py37-chardet-3.0.4_3, py37-click-7.0, py37-coloredlogs-14.0, py37-colormath-3.0.0_1, py37-cryptography-2.6.1, py37-dateutil-2.8.1, py37-decorator-4.4.2, py37-kiwisolver-1.1.0,1, py37-lzstring-1.0.4, py37-markdown-2.6.11_1, py37-matplotlib-2.2.4_2, py37-pycparser-2.20, py37-scikit-sparse-0.4.4_3, py37-simplejson-3.17.0, py37-spectra-0.0.11, py37-tkinter-3.7.8_6, py37-urllib3-1.25.7,1, py37-yaml-5.3.1, py38-numpy-1.16.6,1, python27-2.7.18_1, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3, tcl86-8.6.10, tiff-4.1.0, tk86-8.6.10_1, wayland-1.18.0_4, webp-1.1.0, xorg-fonts-truetype-7.7_1, xorgproto-2020.1
Also listed in: Python

py27-pandas-charm-0.3.0_1
Library for getting character matrices into and out of pandas
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Maintained by: yuri@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, libedit-3.1.20191231,1, libffi-3.3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, py27-numexpr-2.7.1, py27-pytz-2020.1,1, py27-setuptools-44.0.0, py27-six-1.14.0, py35-sqlite3-3.5.9_7, py37-bottleneck-1.3.2, py37-dateutil-2.8.1, py37-pandas-0.24.2_1,1, py38-numpy-1.16.6,1, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, sqlite3-3.32.3_2,1, suitesparse-5.8.1, tbb-2020.3
Also listed in: Python

py27-pyfaidx-0.5.5.2_1
Efficient pythonic random access to fasta subsequences
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Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.21, indexinfo-0.3.1, libffi-3.3, py27-setuptools-44.0.0, py27-six-1.14.0, python27-2.7.18_1, readline-8.0.4
Also listed in: Python

py27-pyfasta-0.5.2_4
Fast, memory-efficient, pythonic access to fasta sequence files
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Maintained by: wen@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, libffi-3.3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, py27-setuptools-44.0.0, py38-numpy-1.16.6,1, python27-2.7.18_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3
Also listed in: Python

py27-pysam-0.16.0
Python module for reading, manipulating and writing genomic data sets
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Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, libffi-3.3, py27-setuptools-44.0.0, py35-cython-0.29.15, python27-2.7.18_1, python35-3.5.9_6, readline-8.0.4
Also listed in: Python

py27-python-nexus-1.63
Generic nexus file format reader for python
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Maintained by: wen@FreeBSD.org
Requires: gettext-runtime-0.21, indexinfo-0.3.1, libffi-3.3, py27-setuptools-44.0.0, python27-2.7.18_1, readline-8.0.4
Also listed in: Python

py27-xenaPython-1.0.10
API for Xena Hub to access genetic information shared through the hub
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Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.21, indexinfo-0.3.1, libffi-3.3, py27-setuptools-44.0.0, python27-2.7.18_1, readline-8.0.4
Also listed in: Python

py37-Genesis-PyAPI-1.2.1
API for the Genesis platform for genetics information processing
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Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.21, indexinfo-0.3.1, libffi-3.3, py27-asn1crypto-1.3.0, py27-idna-2.8, py27-openssl-19.0.0, py27-pysocks-1.7.1, py27-requests-2.22.0, py27-setuptools-44.0.0, py27-six-1.14.0, py27-slumber-0.7.1, py37-certifi-2020.6.20, py37-cffi-1.14.1, py37-chardet-3.0.4_3, py37-cryptography-2.6.1, py37-pycparser-2.20, py37-urllib3-1.25.7,1, python27-2.7.18_1, python37-3.7.8_1, readline-8.0.4
Also listed in: Python

py37-biopython-1.77
Collection of Python modules for bioinformatics
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Maintained by: mauricio@arareko.net
Requires: adobe-cmaps-20051217_4, expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gcc9-9.3.0_1, gettext-runtime-0.21, giflib-5.2.1, gmp-6.2.0, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.4, lcms2-2.11_1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXft-2.3.3, libXrender-0.9.10_2, libffi-3.3, libfontenc-1.1.4, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, metis-5.1.0_8, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, openjpeg-2.3.1, png-1.6.37, py27-olefile-0.46, py27-setuptools-44.0.0, py37-pillow-7.0.0, py37-reportlab-3.5.21_1, py37-tkinter-3.7.8_6, py38-numpy-1.16.6,1, python27-2.7.18_1, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3, tcl86-8.6.10, tiff-4.1.0, tk86-8.6.10_1, webp-1.1.0, xorgproto-2020.1
Also listed in: Python

py37-bx-python-0.8.9
Python module for reading, manipulating and writing genomic data sets
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Maintained by: yuri@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, libffi-3.3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, py27-setuptools-44.0.0, py27-six-1.14.0, py35-cython-0.29.15, py38-numpy-1.16.6,1, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3
Also listed in: Python

py37-chainer-chemistry-0.7.0
Library for deep learning in biology and chemistry
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Maintained by: yuri@FreeBSD.org
Requires: expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXft-2.3.3, libXrender-0.9.10_2, libedit-3.1.20191231,1, libffi-3.3, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, png-1.6.37, protobuf-3.12.3,1, py27-backports_abc-0.5, py27-cycler-0.10.0, py27-futures-3.3.0, py27-numexpr-2.7.1, py27-protobuf-3.12.2,1, py27-pyparsing-2.4.7, py27-pytz-2020.1,1, py27-scipy-1.2.2_1, py27-setuptools-44.0.0, py27-singledispatch-3.4.0.3_1, py27-six-1.14.0, py27-tornado-5.1.1, py27-typing-3.7.4.1, py27-typing-extensions-3.7.4.2, py35-sqlite3-3.5.9_7, py37-bottleneck-1.3.2, py37-chainer-7.2.0_1, py37-dateutil-2.8.1, py37-filelock-3.0.12, py37-joblib-0.13.0, py37-kiwisolver-1.1.0,1, py37-matplotlib-2.2.4_2, py37-pandas-0.24.2_1,1, py37-scikit-learn-0.22_1, py37-tkinter-3.7.8_6, py37-tqdm-4.48.0, py38-numpy-1.16.6,1, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, sqlite3-3.32.3_2,1, suitesparse-5.8.1, tbb-2020.3, tcl86-8.6.10, tk86-8.6.10_1, xorgproto-2020.1
Also listed in: Science

py37-cutadapt-2.7
Trim adapters from high-throughput sequencing reads
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Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.21, indexinfo-0.3.1, libffi-3.3, pigz-2.4, py27-setuptools-44.0.0, py35-cython-0.29.15, py37-bz2file-0.98, py37-dnaio-0.4.2, py37-setuptools_scm-3.4.3, py37-toml-0.10.0, py37-xopen-0.8.4, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, readline-8.0.4, zopfli-1.0.3_1
Also listed in: Python

py37-deap-1.3.1
Distributed Evolutionary Algorithms in Python
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Maintained by: yuri@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, libffi-3.3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, py27-setuptools-44.0.0, py38-numpy-1.16.6,1, python27-2.7.18_1, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3
Also listed in: Math, Science, Devel, Python

py37-dnaio-0.4.2
Read and write FASTQ and FASTA
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Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.21, indexinfo-0.3.1, libffi-3.3, py27-setuptools-44.0.0, py37-setuptools_scm-3.4.3, py37-toml-0.10.0, python27-2.7.18_1, python37-3.7.8_1, readline-8.0.4
Also listed in: Python

py37-ete3-3.1.1
Framework for the analysis and visualization of trees
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: avahi-app-0.7_3, ca_root_nss-3.55, cups-2.3.3_1, dbus-1.12.20, dbus-glib-0.110, double-conversion-3.1.5.19, etc_os-release-0.1_3, expat-2.2.8, fontconfig-2.13.92_2,1, freeglut-3.0.0_2, freetype2-2.10.2, gcc9-9.3.0_1, gdbm-1.18.1_1, gettext-runtime-0.21, giflib-5.2.1, glib-2.56.3_9,1, gmp-6.2.0, gnome_subr-1.0, gnutls-3.6.14, gobject-introspection-1.56.1_1,1, graphite2-1.3.14, harfbuzz-2.6.8, hicolor-icon-theme-0.17, icu-67.1,1, indexinfo-0.3.1, jasper-2.0.16_1, jbigkit-2.1_1, jpeg-turbo-2.0.4, lcms-1.19_6,1, libGLU-9.0.1, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXmu-1.1.3,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.102,1, libepoll-shim-0.0.20200602, libevdev-1.5.9_1, libffi-3.3, libgcrypt-1.8.5, libgpg-error-1.38, libgudev-230_1, libiconv-1.16, libidn2-2.3.0_1, libinput-1.15.6, liblz4-1.9.2_1,1, libmng-1.0.10_3, libmtdev-1.1.5_2, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.16.0, libudev-devd-0.4.2, libunistring-0.9.10_1, libunwind-20200331, libwacom-1.4.1, libxcb-1.13.1, libxkbcommon-0.10.0_2, libxml2-2.9.10, libxshmfence-1.3, libxslt-1.1.34_1, mesa-libs-19.0.8_2, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, nettle-3.6, openblas-0.3.9_2,1, p11-kit-0.23.20_1, pciids-20200624, pcre-8.44, pcre2-10.35, png-1.6.37, py27-enum34-1.1.6, py27-evdev-0.8.1_1, py27-pyudev-0.22.0, py27-qt5-core-5.13.1_1, py27-qt5-gui-5.13.1_1, py27-qt5-opengl-5.13.1_1, py27-qt5-svg-5.13.1_1, py27-qt5-widgets-5.13.1_1, py27-setuptools-44.0.0, py27-sip-4.19.21,1, py27-six-1.14.0, py37-lxml-4.5.2, py37-qt5-printsupport-5.13.1_1, py38-numpy-1.16.6,1, python27-2.7.18_1, python37-3.7.8_1, python38-3.8.5, qscintilla2-qt5-2.11.4, qt5-core-5.15.0_2, qt5-dbus-5.15.0, qt5-gui-5.15.0, qt5-imageformats-5.15.0, qt5-network-5.15.0, qt5-opengl-5.15.0, qt5-printsupport-5.15.0, qt5-svg-5.15.0, qt5-widgets-5.15.0, qtchooser-66_3, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3, tiff-4.1.0, tpm-emulator-0.7.4_2, trousers-0.3.14_2, vulkan-headers-1.2.135.0, wayland-1.18.0_4, webp-1.1.0, xcb-util-0.4.0_2,1, xcb-util-image-0.4.0_1, xcb-util-keysyms-0.4.0_1, xcb-util-renderutil-0.3.9_1, xcb-util-wm-0.4.1_3, xdg-utils-1.1.3_1, xkeyboard-config-2.30, xorgproto-2020.1, xprop-1.2.4, xset-1.2.4_3, zstd-1.4.5
Also listed in: Python

py37-fastTSNE-0.2.13_4
Fast, parallel implementations of t-SNE
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: fftw3-3.3.8_6, gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, libedit-3.1.20191231,1, libffi-3.3, libxml2-2.9.10, llvm80-8.0.1_4, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, perl5-5.32.0, py27-enum34-1.1.6, py27-llvmlite-0.31.0, py27-numba-0.47.0_3, py27-scipy-1.2.2_1, py27-setuptools-44.0.0, py27-singledispatch-3.4.0.3_1, py27-six-1.14.0, py37-funcsigs-1.0.2, py37-joblib-0.13.0, py37-scikit-learn-0.22_1, py38-numpy-1.16.6,1, python27-2.7.18_1, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3
Also listed in: Python

py37-gffutils-0.10.1
Work with GFF and GTF files in a flexible database framework
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.21, indexinfo-0.3.1, libffi-3.3, py27-argh-0.26.2, py27-pyfaidx-0.5.5.2_1, py27-setuptools-44.0.0, py27-six-1.14.0, py37-argcomplete-1.12.0, py37-importlib-metadata-1.7.0, py37-simplejson-3.17.0, py37-zipp-3.1.0, python27-2.7.18_1, python37-3.7.8_1, readline-8.0.4
Also listed in: Python

py37-gtfparse-1.2.1
Parsing tools for GTF (gene transfer format) files
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, libedit-3.1.20191231,1, libffi-3.3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, py27-numexpr-2.7.1, py27-pytz-2020.1,1, py27-setuptools-44.0.0, py27-six-1.14.0, py35-sqlite3-3.5.9_7, py37-bottleneck-1.3.2, py37-dateutil-2.8.1, py37-pandas-0.24.2_1,1, py38-numpy-1.16.6,1, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, sqlite3-3.32.3_2,1, suitesparse-5.8.1, tbb-2020.3
Also listed in: Python

py37-hits-0.1
Utilities for processing high-throughput sequencing experiments
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Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.21, indexinfo-0.3.1, libffi-3.3, py27-setuptools-44.0.0, py35-cython-0.29.15, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, readline-8.0.4
Also listed in: Python

py37-loompy-3.0.6
Work with .loom files for single-cell RNA-seq data
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, hdf-szip-2.1.1, hdf5-1.10.6,1, indexinfo-0.3.1, libedit-3.1.20191231,1, libffi-3.3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, py27-h5py-2.10.0, py27-numexpr-2.7.1, py27-pytz-2020.1,1, py27-scipy-1.2.2_1, py27-setuptools-44.0.0, py27-six-1.14.0, py35-sqlite3-3.5.9_7, py37-bottleneck-1.3.2, py37-dateutil-2.8.1, py37-pandas-0.24.2_1,1, py38-numpy-1.16.6,1, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, sqlite3-3.32.3_2,1, suitesparse-5.8.1, tbb-2020.3
Also listed in: Python

py37-macs2-2.2.7.1
Identify transcription factor binding sites
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, libffi-3.3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, py27-setuptools-44.0.0, py35-cython-0.29.15, py38-numpy-1.16.6,1, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3
Also listed in: Python

py37-multiqc-1.8
Aggregate bioinformatics analysis reports across samples and tools
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: cairo-1.16.0,2, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.8, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.13.92_2,1, freetype2-2.10.2, fribidi-0.19.7, gcc9-9.3.0_1, gettext-runtime-0.21, giflib-5.2.1, glib-2.56.3_9,1, gmp-6.2.0, graphite2-1.3.14, graphviz-2.44.1, harfbuzz-2.6.8, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.4, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXaw-1.0.13_3,2, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.3, libXmu-1.1.3,1, libXpm-3.5.13, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libdrm-2.4.102,1, libepoll-shim-0.0.20200602, libffi-3.3, libfontenc-1.1.4, libgd-2.3.0,1, libiconv-1.16, libltdl-2.4.6, libpciaccess-0.16, libpthread-stubs-0.4, libunwind-20200331, libxcb-1.13.1, libxml2-2.9.10, libxshmfence-1.3, mesa-libs-19.0.8_2, metis-5.1.0_8, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, pango-1.42.4_4, pciids-20200624, pcre-8.44, pixman-0.40.0, png-1.6.37, py27-Babel-2.8.0, py27-Jinja2-2.10.1, py27-MarkupSafe-1.1.1, py27-asn1crypto-1.3.0, py27-backports_abc-0.5, py27-cycler-0.10.0, py27-future-0.18.2, py27-futures-3.3.0, py27-humanfriendly-7.1.1, py27-idna-2.8, py27-monotonic-1.5, py27-networkx-2.1,1, py27-openssl-19.0.0, py27-pygraphviz-1.5, py27-pyparsing-2.4.7, py27-pysocks-1.7.1, py27-pytz-2020.1,1, py27-requests-2.22.0, py27-scipy-1.2.2_1, py27-setuptools-44.0.0, py27-singledispatch-3.4.0.3_1, py27-six-1.14.0, py27-tornado-5.1.1, py37-certifi-2020.6.20, py37-cffi-1.14.1, py37-chardet-3.0.4_3, py37-click-7.0, py37-coloredlogs-14.0, py37-colormath-3.0.0_1, py37-cryptography-2.6.1, py37-dateutil-2.8.1, py37-decorator-4.4.2, py37-kiwisolver-1.1.0,1, py37-lzstring-1.0.4, py37-markdown-2.6.11_1, py37-matplotlib-2.2.4_2, py37-pycparser-2.20, py37-scikit-sparse-0.4.4_3, py37-simplejson-3.17.0, py37-spectra-0.0.11, py37-tkinter-3.7.8_6, py37-urllib3-1.25.7,1, py37-yaml-5.3.1, py38-numpy-1.16.6,1, python27-2.7.18_1, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3, tcl86-8.6.10, tiff-4.1.0, tk86-8.6.10_1, wayland-1.18.0_4, webp-1.1.0, xorg-fonts-truetype-7.7_1, xorgproto-2020.1
Also listed in: Python

py37-orange3-bioinformatics-3.2.2_3
Orange add-on providing common functionality for bioinformatics
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: alsa-lib-1.1.2_2, alsa-plugins-1.1.1_6, aom-2.0.0_1, argp-standalone-1.3_4, avahi-app-0.7_3, ca_root_nss-3.55, cairo-1.16.0,2, cups-2.3.3_1, dav1d-0.7.1, dbus-1.12.20, dbus-glib-0.110, dejavu-2.37_1, double-conversion-3.1.5.19, encodings-1.0.5,1, etc_os-release-0.1_3, expat-2.2.8, ffmpeg-4.3.1_1,1, fftw3-3.3.8_6, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.13.92_2,1, freeglut-3.0.0_2, freetype2-2.10.2, fribidi-0.19.7, gcc9-9.3.0_1, gdbm-1.18.1_1, gettext-runtime-0.21, giflib-5.2.1, glib-2.56.3_9,1, gmp-6.2.0, gnome_subr-1.0, gnutls-3.6.14, gobject-introspection-1.56.1_1,1, graphite2-1.3.14, graphviz-2.44.1, harfbuzz-2.6.8, hicolor-icon-theme-0.17, icu-67.1,1, indexinfo-0.3.1, jasper-2.0.16_1, jbigkit-2.1_1, jpeg-turbo-2.0.4, jsoncpp-1.9.3, lcms-1.19_6,1, lcms2-2.11_1, libGLU-9.0.1, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXaw-1.0.13_3,2, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.3, libXi-1.7.10,1, libXmu-1.1.3,1, libXpm-3.5.13, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libXxf86vm-1.1.4_3, libass-0.14.0, libdaemon-0.14_1, libdrm-2.4.102,1, libedit-3.1.20191231,1, libepoll-shim-0.0.20200602, libevdev-1.5.9_1, libevent-2.1.12, libffi-3.3, libfontenc-1.1.4, libgcrypt-1.8.5, libgd-2.3.0,1, libgpg-error-1.38, libgudev-230_1, libiconv-1.16, libidn2-2.3.0_1, libinput-1.15.6, libltdl-2.4.6, liblz4-1.9.2_1,1, libmng-1.0.10_3, libmtdev-1.1.5_2, libogg-1.3.4,4, libpaper-1.1.24.4, libpci-3.7.0, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.16.0, libtheora-1.1.1_7, libudev-devd-0.4.2, libunistring-0.9.10_1, libunwind-20200331, libv4l-1.18.0, libva-2.8.0, libvdpau-1.4, libvorbis-1.3.7_2,3, libvpx-1.9.0, libwacom-1.4.1, libx264-0.160.3011, libxcb-1.13.1, libxkbcommon-0.10.0_2, libxml2-2.9.10, libxshmfence-1.3, libxslt-1.1.34_1, llvm80-8.0.1_4, mesa-libs-19.0.8_2, metis-5.1.0_8, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.1.0, nettle-3.6, nspr-4.27, nss-3.55, openblas-0.3.9_2,1, opencv-core-3.4.1_35, openjpeg-2.3.1, opus-1.3.1, orange3-3.19.0_2, p11-kit-0.23.20_1, pango-1.42.4_4, pciids-20200624, pcre-8.44, pcre2-10.35, perl5-5.32.0, pixman-0.40.0, png-1.6.37, py27-asn1crypto-1.3.0, py27-backports_abc-0.5, py27-cycler-0.10.0, py27-enum34-1.1.6, py27-evdev-0.8.1_1, py27-futures-3.3.0, py27-idna-2.8, py27-keyring-18.0.1, py27-keyrings.alt-3.1.1, py27-llvmlite-0.31.0, py27-networkx-2.1,1, py27-numba-0.47.0_3, py27-olefile-0.46, py27-openssl-19.0.0, py27-pygraphviz-1.5, py27-pyparsing-2.4.7, py27-pysocks-1.7.1, py27-python-louvain-0.14, py27-pytz-2020.1,1, py27-pyudev-0.22.0, py27-qt5-core-5.13.1_1, py27-qt5-gui-5.13.1_1, py27-qt5-webchannel-5.13.1_1, py27-qt5-webengine-5.12.1_1, py27-qt5-widgets-5.13.1_1, py27-requests-2.22.0, py27-requests-cache-0.4.13, py27-scipy-1.2.2_1, py27-setuptools-44.0.0, py27-singledispatch-3.4.0.3_1, py27-sip-4.19.21,1, py27-six-1.14.0, py27-slumber-0.7.1, py27-tornado-5.1.1, py37-AnyQt-0.0.10, py37-Genesis-PyAPI-1.2.1, py37-PyOpenGL-3.1.5, py37-SecretStorage-2.3.1, py37-bottleneck-1.3.2, py37-certifi-2020.6.20, py37-cffi-1.14.1, py37-chardet-3.0.4_3, py37-cryptography-2.6.1, py37-dateutil-2.8.1, py37-dbus-1.2.16, py37-decorator-4.4.2, py37-docutils-0.15.2, py37-entrypoints-0.3, py37-fastTSNE-0.2.13_4, py37-funcsigs-1.0.2, py37-joblib-0.13.0, py37-kiwisolver-1.1.0,1, py37-matplotlib-2.2.4_2, py37-pillow-7.0.0, py37-pycparser-2.20, py37-pyqtgraph-0.11.0, py37-qt5-network-5.13.1_1, py37-qt5-printsupport-5.13.1_1, py37-qt5-qml-5.13.1_1, py37-scikit-learn-0.22_1, py37-scikit-sparse-0.4.4_3, py37-serverfiles-0.3.0, py37-tkinter-3.7.8_6, py37-urllib3-1.25.7,1, py37-xlrd-1.2.0_1, py37-yaml-5.3.1, py38-numpy-1.16.6,1, pydbus-common-1.2.16, python27-2.7.18_1, python37-3.7.8_1, python38-3.8.5, qscintilla2-qt5-2.11.4, qt5-assistant-5.15.0, qt5-concurrent-5.15.0, qt5-core-5.15.0_2, qt5-dbus-5.15.0, qt5-declarative-5.15.0_1, qt5-designer-5.15.0, qt5-gui-5.15.0, qt5-help-5.15.0, qt5-imageformats-5.15.0, qt5-location-5.15.0, qt5-network-5.15.0, qt5-printsupport-5.15.0, qt5-serialport-5.15.0, qt5-sql-5.15.0, qt5-sqldrivers-sqlite3-5.15.0, qt5-testlib-5.15.0, qt5-uiplugin-5.15.0, qt5-webchannel-5.15.0, qt5-webengine-5.15.0_2, qt5-widgets-5.15.0, qt5-xml-5.15.0, qtchooser-66_3, re2-20200401, readline-8.0.4, s390x-binutils-2.33.1_3,1, snappy-1.1.8, sqlite3-3.32.3_2,1, suitesparse-5.8.1, tbb-2020.3, tcl86-8.6.10, tiff-4.1.0, tk86-8.6.10_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, vulkan-headers-1.2.135.0, wayland-1.18.0_4, webp-1.1.0, x265-3.2.1_4, xcb-util-0.4.0_2,1, xcb-util-image-0.4.0_1, xcb-util-keysyms-0.4.0_1, xcb-util-renderutil-0.3.9_1, xcb-util-wm-0.4.1_3, xdg-utils-1.1.3_1, xkeyboard-config-2.30, xorg-fonts-truetype-7.7_1, xorgproto-2020.1, xprop-1.2.4, xset-1.2.4_3, xvid-1.3.7,1, zstd-1.4.5
Also listed in: Python

py37-orange3-single-cell-0.8.2_3
Orange add-on for gene expression of single cell data
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: alsa-lib-1.1.2_2, alsa-plugins-1.1.1_6, aom-2.0.0_1, argp-standalone-1.3_4, avahi-app-0.7_3, ca_root_nss-3.55, cairo-1.16.0,2, cups-2.3.3_1, dav1d-0.7.1, dbus-1.12.20, dbus-glib-0.110, dejavu-2.37_1, double-conversion-3.1.5.19, encodings-1.0.5,1, etc_os-release-0.1_3, expat-2.2.8, ffmpeg-4.3.1_1,1, fftw3-3.3.8_6, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.13.92_2,1, freeglut-3.0.0_2, freetype2-2.10.2, fribidi-0.19.7, gcc9-9.3.0_1, gdbm-1.18.1_1, gettext-runtime-0.21, giflib-5.2.1, glib-2.56.3_9,1, gmake-4.3_2, gmp-6.2.0, gnome_subr-1.0, gnutls-3.6.14, gobject-introspection-1.56.1_1,1, graphite2-1.3.14, graphviz-2.44.1, harfbuzz-2.6.8, hdf-szip-2.1.1, hdf5-1.10.6,1, hicolor-icon-theme-0.17, icu-67.1,1, indexinfo-0.3.1, jasper-2.0.16_1, jbigkit-2.1_1, jpeg-turbo-2.0.4, jsoncpp-1.9.3, lcms-1.19_6,1, lcms2-2.11_1, libGLU-9.0.1, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXaw-1.0.13_3,2, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.3, libXi-1.7.10,1, libXmu-1.1.3,1, libXpm-3.5.13, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libXxf86vm-1.1.4_3, libass-0.14.0, libdaemon-0.14_1, libdrm-2.4.102,1, libedit-3.1.20191231,1, libepoll-shim-0.0.20200602, libevdev-1.5.9_1, libevent-2.1.12, libffi-3.3, libfontenc-1.1.4, libgcrypt-1.8.5, libgd-2.3.0,1, libgpg-error-1.38, libgudev-230_1, libiconv-1.16, libidn2-2.3.0_1, libinput-1.15.6, libltdl-2.4.6, liblz4-1.9.2_1,1, libmng-1.0.10_3, libmtdev-1.1.5_2, libogg-1.3.4,4, libpaper-1.1.24.4, libpci-3.7.0, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.16.0, libtheora-1.1.1_7, libudev-devd-0.4.2, libunistring-0.9.10_1, libunwind-20200331, libv4l-1.18.0, libva-2.8.0, libvdpau-1.4, libvorbis-1.3.7_2,3, libvpx-1.9.0, libwacom-1.4.1, libx264-0.160.3011, libxcb-1.13.1, libxkbcommon-0.10.0_2, libxml2-2.9.10, libxshmfence-1.3, libxslt-1.1.34_1, llvm80-8.0.1_4, mesa-libs-19.0.8_2, metis-5.1.0_8, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.1.0, nettle-3.6, nspr-4.27, nss-3.55, openblas-0.3.9_2,1, opencv-core-3.4.1_35, openjpeg-2.3.1, opus-1.3.1, orange3-3.19.0_2, p11-kit-0.23.20_1, pango-1.42.4_4, pciids-20200624, pcre-8.44, pcre2-10.35, perl5-5.32.0, pixman-0.40.0, png-1.6.37, py27-Babel-2.8.0, py27-Jinja2-2.10.1, py27-MarkupSafe-1.1.1, py27-alabaster-0.7.6, py27-asn1crypto-1.3.0, py27-backports_abc-0.5, py27-cycler-0.10.0, py27-enum34-1.1.6, py27-evdev-0.8.1_1, py27-futures-3.3.0, py27-h5py-2.10.0, py27-idna-2.8, py27-imagesize-1.1.0, py27-keyring-18.0.1, py27-keyrings.alt-3.1.1, py27-llvmlite-0.31.0, py27-networkx-2.1,1, py27-numba-0.47.0_3, py27-numexpr-2.7.1, py27-olefile-0.46, py27-openssl-19.0.0, py27-packaging-20.4, py27-pygments-2.5.2, py27-pygraphviz-1.5, py27-pyparsing-2.4.7, py27-pysocks-1.7.1, py27-python-louvain-0.14, py27-pytz-2020.1,1, py27-pyudev-0.22.0, py27-qt5-core-5.13.1_1, py27-qt5-gui-5.13.1_1, py27-qt5-webchannel-5.13.1_1, py27-qt5-webengine-5.12.1_1, py27-qt5-widgets-5.13.1_1, py27-requests-2.22.0, py27-requests-cache-0.4.13, py27-scipy-1.2.2_1, py27-setuptools-44.0.0, py27-singledispatch-3.4.0.3_1, py27-sip-4.19.21,1, py27-six-1.14.0, py27-slumber-0.7.1, py27-snowballstemmer-1.2.1, py27-tornado-5.1.1, py35-sqlite3-3.5.9_7, py37-AnyQt-0.0.10, py37-Genesis-PyAPI-1.2.1, py37-PyOpenGL-3.1.5, py37-SecretStorage-2.3.1, py37-astropy-3.1.2,2, py37-bottleneck-1.3.2, py37-certifi-2020.6.20, py37-cffi-1.14.1, py37-chardet-3.0.4_3, py37-cryptography-2.6.1, py37-dateutil-2.8.1, py37-dbus-1.2.16, py37-decorator-4.4.2, py37-docutils-0.15.2, py37-entrypoints-0.3, py37-fastTSNE-0.2.13_4, py37-fastdtw-0.3.4, py37-funcsigs-1.0.2, py37-joblib-0.13.0, py37-kiwisolver-1.1.0,1, py37-loompy-3.0.6, py37-matplotlib-2.2.4_2, py37-orange3-bioinformatics-3.2.2_3, py37-pandas-0.24.2_1,1, py37-pillow-7.0.0, py37-pycparser-2.20, py37-pyqtgraph-0.11.0, py37-pystemmer-2.0.0.1, py37-qt5-network-5.13.1_1, py37-qt5-printsupport-5.13.1_1, py37-qt5-qml-5.13.1_1, py37-scikit-learn-0.22_1, py37-scikit-sparse-0.4.4_3, py37-serverfiles-0.3.0, py37-sphinx-3.1.2,1, py37-sphinxcontrib-applehelp-1.0.2, py37-sphinxcontrib-devhelp-1.0.2, py37-sphinxcontrib-htmlhelp-1.0.3, py37-sphinxcontrib-jsmath-1.0.1, py37-sphinxcontrib-qthelp-1.0.3, py37-sphinxcontrib-serializinghtml-1.1.4, py37-tkinter-3.7.8_6, py37-urllib3-1.25.7,1, py37-xlrd-1.2.0_1, py37-yaml-5.3.1, py38-numpy-1.16.6,1, pydbus-common-1.2.16, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, python38-3.8.5, qscintilla2-qt5-2.11.4, qt5-assistant-5.15.0, qt5-concurrent-5.15.0, qt5-core-5.15.0_2, qt5-dbus-5.15.0, qt5-declarative-5.15.0_1, qt5-designer-5.15.0, qt5-gui-5.15.0, qt5-help-5.15.0, qt5-imageformats-5.15.0, qt5-location-5.15.0, qt5-network-5.15.0, qt5-printsupport-5.15.0, qt5-serialport-5.15.0, qt5-sql-5.15.0, qt5-sqldrivers-sqlite3-5.15.0, qt5-testlib-5.15.0, qt5-uiplugin-5.15.0, qt5-webchannel-5.15.0, qt5-webengine-5.15.0_2, qt5-widgets-5.15.0, qt5-xml-5.15.0, qtchooser-66_3, re2-20200401, readline-8.0.4, s390x-binutils-2.33.1_3,1, snappy-1.1.8, sqlite3-3.32.3_2,1, suitesparse-5.8.1, tbb-2020.3, tcl86-8.6.10, tiff-4.1.0, tk86-8.6.10_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, vulkan-headers-1.2.135.0, wayland-1.18.0_4, webp-1.1.0, x265-3.2.1_4, xcb-util-0.4.0_2,1, xcb-util-image-0.4.0_1, xcb-util-keysyms-0.4.0_1, xcb-util-renderutil-0.3.9_1, xcb-util-wm-0.4.1_3, xdg-utils-1.1.3_1, xkeyboard-config-2.30, xorg-fonts-truetype-7.7_1, xorgproto-2020.1, xprop-1.2.4, xset-1.2.4_3, xvid-1.3.7,1, zstd-1.4.5
Also listed in: Python

py37-pandas-charm-0.3.0_1
Library for getting character matrices into and out of pandas
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, libedit-3.1.20191231,1, libffi-3.3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, py27-numexpr-2.7.1, py27-pytz-2020.1,1, py27-setuptools-44.0.0, py27-six-1.14.0, py35-sqlite3-3.5.9_7, py37-bottleneck-1.3.2, py37-dateutil-2.8.1, py37-pandas-0.24.2_1,1, py38-numpy-1.16.6,1, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, sqlite3-3.32.3_2,1, suitesparse-5.8.1, tbb-2020.3
Also listed in: Python

py37-pyfaidx-0.5.5.2_1
Efficient pythonic random access to fasta subsequences
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.21, indexinfo-0.3.1, libffi-3.3, py27-setuptools-44.0.0, py27-six-1.14.0, python27-2.7.18_1, python37-3.7.8_1, readline-8.0.4
Also listed in: Python

py37-pyfasta-0.5.2_4
Fast, memory-efficient, pythonic access to fasta sequence files
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, libffi-3.3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, py27-setuptools-44.0.0, py38-numpy-1.16.6,1, python27-2.7.18_1, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3
Also listed in: Python

py37-pymol-2.4.0
OpenGL-based molecular visualization system
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Maintained by: yuri@FreeBSD.org
Requires: avahi-app-0.7_3, blt-2.5.3_5, ca_root_nss-3.55, cups-2.3.3_1, curl-7.71.1, dbus-1.12.20, dbus-glib-0.110, double-conversion-3.1.5.19, etc_os-release-0.1_3, expat-2.2.8, fontconfig-2.13.92_2,1, freeglut-3.0.0_2, freetype2-2.10.2, gcc9-9.3.0_1, gdbm-1.18.1_1, gettext-runtime-0.21, giflib-5.2.1, glew-2.2.0, glib-2.56.3_9,1, glm-0.9.8.5_4,1, gmp-6.2.0, gnome_subr-1.0, gnutls-3.6.14, gobject-introspection-1.56.1_1,1, graphite2-1.3.14, harfbuzz-2.6.8, hdf-szip-2.1.1, hdf5-1.10.6,1, hicolor-icon-theme-0.17, icu-67.1,1, indexinfo-0.3.1, jasper-2.0.16_1, jbigkit-2.1_1, jpeg-turbo-2.0.4, lcms-1.19_6,1, libGLU-9.0.1, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.3, libXi-1.7.10,1, libXmu-1.1.3,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.102,1, libepoll-shim-0.0.20200602, libevdev-1.5.9_1, libffi-3.3, libgudev-230_1, libiconv-1.16, libidn2-2.3.0_1, libinput-1.15.6, liblz4-1.9.2_1,1, libmng-1.0.10_3, libmtdev-1.1.5_2, libnghttp2-1.41.0, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.16.0, libudev-devd-0.4.2, libunistring-0.9.10_1, libunwind-20200331, libwacom-1.4.1, libxcb-1.13.1, libxkbcommon-0.10.0_2, libxml2-2.9.10, libxshmfence-1.3, mesa-libs-19.0.8_2, metis-5.1.0_8, mmtf-cpp-1.0.0_2, mpc-1.1.0_2, mpfr-4.1.0, msgpack-3.3.0, netcdf-4.7.3, nettle-3.6, openblas-0.3.9_2,1, p11-kit-0.23.20_1, pciids-20200624, pcre-8.44, pcre2-10.35, pkgconf-1.7.3,1, png-1.6.37, py27-enum34-1.1.6, py27-evdev-0.8.1_1, py27-msgpack-0.6.2, py27-pyudev-0.22.0, py27-qt5-core-5.13.1_1, py27-qt5-gui-5.13.1_1, py27-qt5-opengl-5.13.1_1, py27-qt5-widgets-5.13.1_1, py27-setuptools-44.0.0, py27-sip-4.19.21,1, py27-six-1.14.0, py37-Pmw-2.0.1_1, py37-tkinter-3.7.8_6, py38-numpy-1.16.6,1, python27-2.7.18_1, python37-3.7.8_1, python38-3.8.5, qscintilla2-qt5-2.11.4, qt5-core-5.15.0_2, qt5-dbus-5.15.0, qt5-gui-5.15.0, qt5-imageformats-5.15.0, qt5-network-5.15.0, qt5-opengl-5.15.0, qt5-printsupport-5.15.0, qt5-widgets-5.15.0, qtchooser-66_3, readline-8.0.4, s390x-binutils-2.33.1_3,1, suitesparse-5.8.1, tbb-2020.3, tcl86-8.6.10, tiff-4.1.0, tk86-8.6.10_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, vulkan-headers-1.2.135.0, wayland-1.18.0_4, webp-1.1.0, xcb-util-0.4.0_2,1, xcb-util-image-0.4.0_1, xcb-util-keysyms-0.4.0_1, xcb-util-renderutil-0.3.9_1, xcb-util-wm-0.4.1_3, xdg-utils-1.1.3_1, xkeyboard-config-2.30, xorgproto-2020.1, xprop-1.2.4, xset-1.2.4_3, zstd-1.4.5
Also listed in: Science, Python

py37-pysam-0.16.0
Python module for reading, manipulating and writing genomic data sets
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, libffi-3.3, py27-setuptools-44.0.0, py35-cython-0.29.15, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, readline-8.0.4
Also listed in: Python

py37-python-nexus-1.63
Generic nexus file format reader for python
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: gettext-runtime-0.21, indexinfo-0.3.1, libffi-3.3, py27-setuptools-44.0.0, python27-2.7.18_1, python37-3.7.8_1, readline-8.0.4
Also listed in: Python

py37-scikit-bio-0.5.6
Data structures, algorithms, educational resources for bioinformatics
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXft-2.3.3, libXrender-0.9.10_2, libedit-3.1.20191231,1, libffi-3.3, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, png-1.6.37, py27-asn1crypto-1.3.0, py27-backcall-0.2.0, py27-backports_abc-0.5, py27-cycler-0.10.0, py27-futures-3.3.0, py27-hdmedians-0.13, py27-idna-2.8, py27-lockfile-0.12.2, py27-msgpack-0.6.2, py27-numexpr-2.7.1, py27-openssl-19.0.0, py27-parso-0.7.1, py27-pexpect-4.8.0, py27-ptyprocess-0.6.0, py27-pygments-2.5.2, py27-pyparsing-2.4.7, py27-pysocks-1.7.1, py27-pytz-2020.1,1, py27-requests-2.22.0, py27-scipy-1.2.2_1, py27-setuptools-44.0.0, py27-singledispatch-3.4.0.3_1, py27-six-1.14.0, py27-tornado-5.1.1, py27-wcwidth-0.1.8, py35-sqlite3-3.5.9_7, py37-CacheControl-0.12.6, py37-bottleneck-1.3.2, py37-certifi-2020.6.20, py37-cffi-1.14.1, py37-chardet-3.0.4_3, py37-cryptography-2.6.1, py37-dateutil-2.8.1, py37-decorator-4.4.2, py37-ipython-7.16.1, py37-ipython_genutils-0.2.0, py37-jedi-0.17.1, py37-joblib-0.13.0, py37-kiwisolver-1.1.0,1, py37-matplotlib-2.2.4_2, py37-natsort-7.0.1, py37-pandas-0.24.2_1,1, py37-pickleshare-0.7.5, py37-prompt_toolkit-3.0.5, py37-pycparser-2.20, py37-scikit-learn-0.22_1, py37-tkinter-3.7.8_6, py37-traitlets-4.3.3, py37-urllib3-1.25.7,1, py38-numpy-1.16.6,1, python27-2.7.18_1, python35-3.5.9_6, python37-3.7.8_1, python38-3.8.5, readline-8.0.4, s390x-binutils-2.33.1_3,1, sqlite3-3.32.3_2,1, suitesparse-5.8.1, tbb-2020.3, tcl86-8.6.10, tk86-8.6.10_1, xorgproto-2020.1
Also listed in: Python

py37-xenaPython-1.0.10
API for Xena Hub to access genetic information shared through the hub
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.21, indexinfo-0.3.1, libffi-3.3, py27-setuptools-44.0.0, python27-2.7.18_1, python37-3.7.8_1, readline-8.0.4
Also listed in: Python

rainbow-2.0.4
Efficient clustering and assembling of short reads, especially for RAD
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1

raster3d-3.0.3_7
Set of tools for generating raster images of proteins and molecules
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: ImageMagick6-6.9.11.6,1, avahi-app-0.7_3, ca_root_nss-3.55, cairo-1.16.0,2, cups-2.3.3_1, dbus-1.12.20, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.8, fftw3-3.3.8_6, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.13.92_2,1, freetype2-2.10.2, fribidi-0.19.7, gcc9-9.3.0_1, gdbm-1.18.1_1, gdk-pixbuf2-2.40.0, gettext-runtime-0.21, ghostscript9-agpl-base-9.52_6, ghostscript9-agpl-x11-9.52, giflib-5.2.1, glib-2.56.3_9,1, gmp-6.2.0, gnome_subr-1.0, gnutls-3.6.14, gobject-introspection-1.56.1_1,1, graphite2-1.3.14, gsfonts-8.11_8, harfbuzz-2.6.8, indexinfo-0.3.1, jbig2dec-0.18, jbigkit-2.1_1, jpeg-turbo-2.0.4, lcms2-2.11_1, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.3, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libcroco-0.6.13, libdaemon-0.14_1, libdrm-2.4.102,1, libepoll-shim-0.0.20200602, libffi-3.3, libfontenc-1.1.4, libgd-2.3.0,1, libgsf-1.14.47_1, libiconv-1.16, libidn-1.35, libidn2-2.3.0_1, liblqr-1-0.4.2, libltdl-2.4.6, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libraqm-0.6.0, libraw-0.19.5, librsvg2-2.40.21, libtasn1-4.16.0, libunistring-0.9.10_1, libunwind-20200331, libwmf-0.2.8.4_15, libxcb-1.13.1, libxml2-2.9.10, libxshmfence-1.3, mesa-libs-19.0.8_2, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.1.0, nettle-3.6, openjpeg-2.3.1, p11-kit-0.23.20_1, pango-1.42.4_4, pciids-20200624, pcre-8.44, perl5-5.32.0, pixman-0.40.0, pkgconf-1.7.3,1, png-1.6.37, poppler-data-0.4.9_4, python37-3.7.8_1, readline-8.0.4, s390x-binutils-2.33.1_3,1, shared-mime-info-1.10_2, tiff-4.1.0, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.18.0_4, webp-1.1.0, xorg-fonts-truetype-7.7_1, xorgproto-2020.1
Also listed in: Graphics

recombine-1.41_2
Program to fit population models across sites
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

rna-STAR-2.7.3.a
Spliced Transcripts Alignment to a Reference
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmake-4.3_2, gmp-6.2.0, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.1.0, s390x-binutils-2.33.1_3,1

ruby26-bio-1.5.1
Integrated environment for Bioinformatics written in Ruby
Long description | Changes | Main Web Site
Maintained by: mauricio@arareko.net
Requires: indexinfo-0.3.1, libedit-3.1.20191231,1, libffi-3.3, libunwind-20200331, libyaml-0.2.5, ruby-2.6.6_1,1
Also listed in: Ruby

rubygem-bio-2.0.1
Integrated environment for Bioinformatics written in Ruby
Long description | Changes | Main Web Site
Maintained by: ruby@FreeBSD.org
Requires: indexinfo-0.3.1, libedit-3.1.20191231,1, libffi-3.3, libunwind-20200331, libyaml-0.2.5, ruby-2.6.6_1,1, ruby26-gems-3.0.6
Also listed in: Rubygems

rubygem-bio-executables-1.0.0
Collection of miscellaneous utilities for bioinformatics
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: indexinfo-0.3.1, libedit-3.1.20191231,1, libffi-3.3, libunwind-20200331, libyaml-0.2.5, ruby-2.6.6_1,1, ruby26-gems-3.0.6, rubygem-bio-2.0.1, rubygem-bio-old-biofetch-emulator-1.0.0
Also listed in: Rubygems

rubygem-bio-old-biofetch-emulator-1.0.0
Emulate Bio::Fetch object
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: indexinfo-0.3.1, libedit-3.1.20191231,1, libffi-3.3, libunwind-20200331, libyaml-0.2.5, ruby-2.6.6_1,1, ruby26-gems-3.0.6, rubygem-bio-2.0.1
Also listed in: Rubygems

rubygem-bio-shell-1.0.0
Command-line interface on BioRuby
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: indexinfo-0.3.1, libedit-3.1.20191231,1, libffi-3.3, libunwind-20200331, libyaml-0.2.5, ruby-2.6.6_1,1, ruby26-gems-3.0.6, rubygem-bio-2.0.1
Also listed in: Rubygems

samtools-1.10
Tools for manipulating next-generation sequencing data
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, ca_root_nss-3.55, curl-7.71.1, gettext-runtime-0.21, gmake-4.3_2, htslib-1.10.2, indexinfo-0.3.1, libdeflate-1.6, libnghttp2-1.41.0, m4-1.4.18_1,1, perl5-5.32.0

scrm-1.7.4
Coalescent simulator for biological sequences
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, m4-1.4.18_1,1, perl5-5.32.0

seaview-5.0.4
Multiple DNA/protein sequence alignment editor
Long description | Changes | Main Web Site
Maintained by: bofh@FreeBSD.org
Requires: expat-2.2.8, fltk-1.3.5, fontconfig-2.13.92_2,1, freetype2-2.10.2, gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, jpeg-turbo-2.0.4, libGLU-9.0.1, libX11-1.6.10_1,1, libXau-1.0.9, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.3, libXinerama-1.1.4_2,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXxf86vm-1.1.4_3, libdrm-2.4.102,1, libepoll-shim-0.0.20200602, libffi-3.3, libpciaccess-0.16, libpthread-stubs-0.4, libunwind-20200331, libxcb-1.13.1, libxml2-2.9.10, libxshmfence-1.3, mesa-libs-19.0.8_2, pciids-20200624, png-1.6.37, wayland-1.18.0_4, xorgproto-2020.1

seqan-2.4.0
C++ sequence analysis template library
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org

seqan-apps-2.4.0_9
Official bioinformatic applications based on the SeqAn library
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org
Requires: boost-libs-1.72.0_2, ca_root_nss-3.55, cmake-3.17.3_1, curl-7.71.1, expat-2.2.8, gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, icu-67.1,1, indexinfo-0.3.1, jsoncpp-1.9.3, libarchive-3.4.3,1, libffi-3.3, liblz4-1.9.2_1,1, libnghttp2-1.41.0, libuv-1.38.1, lzo2-2.10_1, mpc-1.1.0_2, mpfr-4.1.0, ninja-1.10.0,2, python37-3.7.8_1, readline-8.0.4, rhash-1.3.9, s390x-binutils-2.33.1_3,1

seqan1-1.3.1_4
C++ Sequence Analysis Library
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org

seqio-1.2.2_1
Set of C functions which can read/write biological sequence files
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

seqtk-1.2.8
Tool for processing sequences in FASTA/FASTQ format
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

sim4-2003.09.21_1
Algorithm for aligning expressed DNA with genomic sequences
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

simbody-3.7_3
Multibody dynamics library for (bio)mechanical systems simulation
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: ca_root_nss-3.55, cmake-3.17.3_1, curl-7.71.1, expat-2.2.8, freeglut-3.0.0_2, gcc9-9.3.0_1, gettext-runtime-0.21, gmp-6.2.0, indexinfo-0.3.1, jsoncpp-1.9.3, libGLU-9.0.1, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXmu-1.1.3,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libarchive-3.4.3,1, libdrm-2.4.102,1, libepoll-shim-0.0.20200602, libffi-3.3, liblz4-1.9.2_1,1, libnghttp2-1.41.0, libpciaccess-0.16, libpthread-stubs-0.4, libunwind-20200331, libuv-1.38.1, libxcb-1.13.1, libxml2-2.9.10, libxshmfence-1.3, lzo2-2.10_1, mesa-libs-19.0.8_2, mpc-1.1.0_2, mpfr-4.1.0, openblas-0.3.9_2,1, pciids-20200624, rhash-1.3.9, s390x-binutils-2.33.1_3,1, wayland-1.18.0_4, xorgproto-2020.1
Also listed in: Science

slclust-2010.02.02
Single-linkage clustering with Jaccard similarity
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

smithwaterman-g20160702
Smith-waterman-gotoh alignment algorithm
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1

stacks-2.4_1
Software pipeline for building loci from short-read sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gcc9-9.3.0_1, gettext-runtime-0.21, gmake-4.3_2, gmp-6.2.0, indexinfo-0.3.1, libffi-3.3, mpc-1.1.0_2, mpfr-4.1.0, python37-3.7.8_1, readline-8.0.4, s390x-binutils-2.33.1_3,1
Also listed in: Perl5, Python

stringtie-2.1.1
Transcript assembly and quantification for RNA-seq
Long description | Changes | Main Web Site
Maintained by: mzaki@e-mail.ne.jp
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1

subread-2.0.1
High-performance read alignment, quantification and mutation discovery
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, libsysinfo-0.0.3_2

tRNAscan-SE-2.0.5
Searching for tRNA genes in genomic sequence
Long description | Changes | Main Web Site
Maintained by: mzaki@e-mail.ne.jp
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, indexinfo-0.3.1, infernal-1.1.3, m4-1.4.18_1,1, perl5-5.32.0

tabixpp-1.0.0.10_1
C++ wrapper to tabix indexer
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: ca_root_nss-3.55, curl-7.71.1, htslib-1.10.2, libdeflate-1.6, libnghttp2-1.41.0

tophat-2.1.1_1
Fast splice junction mapper for RNA-Seq reads
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: bash-5.0.18_2, boost-libs-1.72.0_2, bowtie2-2.4.1_2, gettext-runtime-0.21, gmake-4.3_2, icu-67.1,1, indexinfo-0.3.1, libffi-3.3, perl5-5.32.0, python27-2.7.18_1, python37-3.7.8_1, readline-8.0.4, tbb-2020.3
Also listed in: Python

treekin-0.5.1_2
Efficient computation of RNA folding dynamics
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: blas-3.5.0_6, gcc9-9.3.0_1, gettext-runtime-0.21, gmake-4.3_2, gmp-6.2.0, indexinfo-0.3.1, lapack-3.5.0_8, lapacke-3.5.0_8, mpc-1.1.0_2, mpfr-4.1.0, s390x-binutils-2.33.1_3,1

treepuzzle-5.2
Maximum likelihood phylogeny reconstruction using quartets
Long description | Changes | Main Web Site
Maintained by: jan.lentfer@web.de

trimadap-0.1.3
Trim adapter sequences from Illumina data using heuristic rules
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

trimmomatic-0.39
Flexible read trimming tool for Illumina NGS data
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: alsa-lib-1.1.2_2, dejavu-2.37_1, expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gettext-runtime-0.21, giflib-5.2.1, indexinfo-0.3.1, java-zoneinfo-2020.a, javavmwrapper-2.7.5, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_2, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.10, mkfontscale-1.2.1, openjdk8-8.265.01.1, xorgproto-2020.1
Also listed in: Java

ugene-34.0
Free, open-source, cross-platform bioinformatics toolkit
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org
Requires: alsa-lib-1.1.2_2, alsa-plugins-1.1.1_6, aom-2.0.0_1, argp-standalone-1.3_4, avahi-app-0.7_3, bash-5.0.18_2, ca_root_nss-3.55, cups-2.3.3_1, dav1d-0.7.1, dbus-1.12.20, dbus-glib-0.110, desktop-file-utils-0.24, double-conversion-3.1.5.19, etc_os-release-0.1_3, expat-2.2.8, ffmpeg-4.3.1_1,1, fontconfig-2.13.92_2,1, freeglut-3.0.0_2, freetype2-2.10.2, fribidi-0.19.7, gdbm-1.18.1_1, gettext-runtime-0.21, giflib-5.2.1, glib-2.56.3_9,1, gmp-6.2.0, gnome_subr-1.0, gnutls-3.6.14, gobject-introspection-1.56.1_1,1, graphite2-1.3.14, harfbuzz-2.6.8, hicolor-icon-theme-0.17, icu-67.1,1, indexinfo-0.3.1, jasper-2.0.16_1, jbigkit-2.1_1, jpeg-turbo-2.0.4, jsoncpp-1.9.3, lcms-1.19_6,1, lcms2-2.11_1, libGLU-9.0.1, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXmu-1.1.3,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libXxf86vm-1.1.4_3, libass-0.14.0, libdaemon-0.14_1, libdrm-2.4.102,1, libedit-3.1.20191231,1, libepoll-shim-0.0.20200602, libevdev-1.5.9_1, libevent-2.1.12, libffi-3.3, libgcrypt-1.8.5, libgpg-error-1.38, libgudev-230_1, libiconv-1.16, libidn2-2.3.0_1, libinput-1.15.6, liblz4-1.9.2_1,1, libmng-1.0.10_3, libmtdev-1.1.5_2, libogg-1.3.4,4, libpaper-1.1.24.4, libpci-3.7.0, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.16.0, libtheora-1.1.1_7, libudev-devd-0.4.2, libunistring-0.9.10_1, libunwind-20200331, libv4l-1.18.0, libva-2.8.0, libvdpau-1.4, libvorbis-1.3.7_2,3, libvpx-1.9.0, libwacom-1.4.1, libx264-0.160.3011, libxcb-1.13.1, libxkbcommon-0.10.0_2, libxml2-2.9.10, libxshmfence-1.3, libxslt-1.1.34_1, mesa-libs-19.0.8_2, nettle-3.6, nspr-4.27, nss-3.55, opencv-core-3.4.1_35, opus-1.3.1, p11-kit-0.23.20_1, pciids-20200624, pcre-8.44, pcre2-10.35, perl5-5.32.0, png-1.6.37, py27-evdev-0.8.1_1, py27-pyudev-0.22.0, py27-setuptools-44.0.0, py27-six-1.14.0, python27-2.7.18_1, python37-3.7.8_1, qt5-assistant-5.15.0, qt5-buildtools-5.15.0, qt5-concurrent-5.15.0, qt5-core-5.15.0_2, qt5-dbus-5.15.0, qt5-declarative-5.15.0_1, qt5-designer-5.15.0, qt5-gui-5.15.0, qt5-help-5.15.0, qt5-imageformats-5.15.0, qt5-linguisttools-5.15.0, qt5-location-5.15.0, qt5-network-5.15.0, qt5-opengl-5.15.0, qt5-printsupport-5.15.0, qt5-qmake-5.15.0, qt5-script-5.15.0, qt5-scripttools-5.15.0, qt5-serialport-5.15.0, qt5-sql-5.15.0, qt5-sqldrivers-sqlite3-5.15.0, qt5-svg-5.15.0, qt5-testlib-5.15.0, qt5-uiplugin-5.15.0, qt5-webchannel-5.15.0, qt5-webengine-5.15.0_2, qt5-websockets-5.15.0, qt5-widgets-5.15.0, qt5-xml-5.15.0, qtchooser-66_3, re2-20200401, readline-8.0.4, shared-mime-info-1.10_2, snappy-1.1.8, sqlite3-3.32.3_2,1, tiff-4.1.0, tpm-emulator-0.7.4_2, trousers-0.3.14_2, vulkan-headers-1.2.135.0, wayland-1.18.0_4, webp-1.1.0, x265-3.2.1_4, xcb-util-0.4.0_2,1, xcb-util-image-0.4.0_1, xcb-util-keysyms-0.4.0_1, xcb-util-renderutil-0.3.9_1, xcb-util-wm-0.4.1_3, xdg-utils-1.1.3_1, xkeyboard-config-2.30, xorgproto-2020.1, xprop-1.2.4, xset-1.2.4_3, xvid-1.3.7,1, zstd-1.4.5
Also listed in: Science

vcflib-1.0.0.r1.130_1
C++ library and CLI tools for parsing and manipulating VCF files
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: ca_root_nss-3.55, curl-7.71.1, fastahack-1.0.0, filevercmp-g20151117, fsom-g20151117_2, gettext-runtime-0.21, gmake-4.3_2, htslib-1.10.2, indexinfo-0.3.1, intervaltree-g20151213_2, libdeflate-1.6, libffi-3.3, libnghttp2-1.41.0, multichoose-1.0.3.2, python37-3.7.8_1, readline-8.0.4, smithwaterman-g20160702, tabixpp-1.0.0.10_1

vcftools-0.1.16
Tools for working with VCF genomics files
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, m4-1.4.18_1,1, perl5-5.32.0, pkgconf-1.7.3,1

velvet-1.2.10_2
Sequence assembler for very short reads
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp
Requires: gettext-runtime-0.21, gmake-4.3_2, indexinfo-0.3.1, libffi-3.3, perl5-5.32.0, python37-3.7.8_1, readline-8.0.4

viennarna-2.4.14_1
Alignment tools for the structural analysis of RNA
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, bash-5.0.18_2, expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gettext-runtime-0.21, giflib-5.2.1, gmake-4.3_2, gmp-6.2.0, gsl-2.6, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.4, libX11-1.6.10_1,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libgd-2.3.0,1, libpthread-stubs-0.4, libtool-2.4.6_1, libxcb-1.13.1, libxml2-2.9.10, m4-1.4.18_1,1, mpfr-4.1.0, perl5-5.32.0, pkgconf-1.7.3,1, png-1.6.37, readline-8.0.4, tiff-4.1.0, webp-1.1.0, xorgproto-2020.1

vsearch-2.15.0
Versatile open-source tool for metagenomics
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.2, avahi-app-0.7_3, ca_root_nss-3.55, cups-2.3.3_1, dbus-1.12.20, dbus-glib-0.110, expat-2.2.8, fontconfig-2.13.92_2,1, freetype2-2.10.2, gdbm-1.18.1_1, gettext-runtime-0.21, ghostscript9-agpl-base-9.52_6, glib-2.56.3_9,1, gmake-4.3_2, gmp-6.2.0, gnome_subr-1.0, gnutls-3.6.14, gobject-introspection-1.56.1_1,1, indexinfo-0.3.1, jbig2dec-0.18, jbigkit-2.1_1, jpeg-turbo-2.0.4, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.10_1,1, libXau-1.0.9, libXdmcp-1.1.3, libdaemon-0.14_1, libffi-3.3, libiconv-1.16, libidn-1.35, libidn2-2.3.0_1, libpaper-1.1.24.4, libpthread-stubs-0.4, libsysinfo-0.0.3_2, libtasn1-4.16.0, libunistring-0.9.10_1, libxcb-1.13.1, libxml2-2.9.10, m4-1.4.18_1,1, nettle-3.6, p11-kit-0.23.20_1, pcre-8.44, perl5-5.32.0, png-1.6.37, poppler-data-0.4.9_4, python37-3.7.8_1, readline-8.0.4, tiff-4.1.0, tpm-emulator-0.7.4_2, trousers-0.3.14_2, xorgproto-2020.1

vt-0.57721_1
Discovers short variants from Next Generation Sequencing data
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: ca_root_nss-3.55, curl-7.71.1, gettext-runtime-0.21, gmake-4.3_2, htslib-1.10.2, indexinfo-0.3.1, libdeflate-1.6, libnghttp2-1.41.0, libsvm-3.23

wise-2.4.1_1
Intelligent algorithms for DNA searches
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.21, glib-2.56.3_9,1, indexinfo-0.3.1, libffi-3.3, libiconv-1.16, libxml2-2.9.10, pcre-8.44, pkgconf-1.7.3,1, python37-3.7.8_1, readline-8.0.4

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