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|CheckM
 
|CheckM
 
|Quality assessment tool for the microbial genomes
 
|Quality assessment tool for the microbial genomes
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/checkm/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://ecogenomics.github.io/CheckM/]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/checkm/pkg-descr?revision=HEAD]] [[https://ecogenomics.github.io/CheckM/]]
 
|-
 
|-
 
|GroopM
 
|GroopM
 
|Metagenomic binning suite
 
|Metagenomic binning suite
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/groopm/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://ecogenomics.github.io/GroopM/]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/groopm/pkg-descr?revision=HEAD]] [[http://ecogenomics.github.io/GroopM/]]
 
|-
 
|-
 
|InsightToolkit
 
|InsightToolkit
 
|Insight Toolkit
 
|Insight Toolkit
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/InsightToolkit/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.itk.org]]
+
|[[https://svnweb.freebsd.org/ports/head/science/InsightToolkit/pkg-descr?revision=HEAD]] [[http://www.itk.org]]
 
|-
 
|-
 
|Jellyfish
 
|Jellyfish
 
|Fast, memory-efficient counting of k-mers in DNA
 
|Fast, memory-efficient counting of k-mers in DNA
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/jellyfish/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.genome.umd.edu/jellyfish.html]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/jellyfish/pkg-descr?revision=HEAD]] [[http://www.genome.umd.edu/jellyfish.html]]
 
|-
 
|-
 
|abyss
 
|abyss
 
|Assembly By Short Sequences: parallel, paired-end sequence assembler
 
|Assembly By Short Sequences: parallel, paired-end sequence assembler
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/afni/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://afni.nimh.nih.gov/afni/]]
+
|[[https://svnweb.freebsd.org/ports/head/science/afni/pkg-descr?revision=HEAD]] [[http://afni.nimh.nih.gov/afni/]]
 
|-
 
|-
 
|afni
 
|afni
 
|Advanced Functional Neuro Imaging
 
|Advanced Functional Neuro Imaging
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/afni/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://afni.nimh.nih.gov/afni/]]
+
|[[https://svnweb.freebsd.org/ports/head/science/afni/pkg-descr?revision=HEAD]] [[http://afni.nimh.nih.gov/afni/]]
 
|-
 
|-
 
|artemis
 
|artemis
 
|DNA sequence viewer and annotation tool
 
|DNA sequence viewer and annotation tool
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/artemis/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.sanger.ac.uk/science/tools/artemis]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/artemis/pkg-descr?revision=HEAD]] [[https://www.sanger.ac.uk/science/tools/artemis]]
 
|-
 
|-
 
|avida
 
|avida
 
|Auto-adaptive genetic system designed for ALife research
 
|Auto-adaptive genetic system designed for ALife research
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/avida/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://avida.devosoft.org/]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/avida/pkg-descr?revision=HEAD]] [[http://avida.devosoft.org/]]
 
|-
 
|-
 
|babel
 
|babel
 
|Converts among various molecular file formats
 
|Converts among various molecular file formats
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/babel/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://smog.com/chem/babel/]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/babel/pkg-descr?revision=HEAD]] [[http://smog.com/chem/babel/]]
 
|-
 
|-
 
|bamtools
 
|bamtools
 
|API and toolkit for handling BAM files
 
|API and toolkit for handling BAM files
−
|[[File:1329059652.png|35px|link=https://github.com/pezmaster31/bamtools]]
+
|[[https://github.com/pezmaster31/bamtools]]
 
|-
 
|-
 
|biococoa
 
|biococoa
 
|Bioinformatics framework
 
|Bioinformatics framework
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/biococoa/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://bioinformatics.org/biococoa/]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/biococoa/pkg-descr?revision=HEAD]] [[http://bioinformatics.org/biococoa/]]
 
|-
 
|-
 
|canu
 
|canu
 
|Single molecule sequence assembler
 
|Single molecule sequence assembler
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/canu/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://canu.readthedocs.io/]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/canu/pkg-descr?revision=HEAD]] [[https://canu.readthedocs.io/]]
 
|-
 
|-
 
|cycle
 
|cycle
 
|Calendar program for women
 
|Calendar program for women
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/deskutils/cycle/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://cycle.sourceforge.net/]]
+
|[[https://svnweb.freebsd.org/ports/head/deskutils/cycle/pkg-descr?revision=HEAD]] [[http://cycle.sourceforge.net/]]
 
|-
 
|-
 
|cytoscape
 
|cytoscape
 
|Software to visualize molecular interaction networks, gene expression
 
|Software to visualize molecular interaction networks, gene expression
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/cytoscape/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.cytoscape.org]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/cytoscape/pkg-descr?revision=HEAD]] [[http://www.cytoscape.org]]
 
|-
 
|-
 
|dDocent
 
|dDocent
 
|Bash pipeline for RAD sequencing
 
|Bash pipeline for RAD sequencing
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/ddocent/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://ddocent.com]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/ddocent/pkg-descr?revision=HEAD]] [[http://ddocent.com]]
 
|-
 
|-
 
|emboss
 
|emboss
 
|Collection of open source tools for genetic sequence analysis
 
|Collection of open source tools for genetic sequence analysis
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/emboss/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.emboss.org/]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/emboss/pkg-descr?revision=HEAD]] [[http://www.emboss.org/]]
 
|-
 
|-
 
|figtree
 
|figtree
 
|Graphical viewer of phylogenetic trees
 
|Graphical viewer of phylogenetic trees
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/figtree/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://tree.bio.ed.ac.uk/software/figtree/]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/figtree/pkg-descr?revision=HEAD]] [[http://tree.bio.ed.ac.uk/software/figtree/]]
 
|-
 
|-
 
|garlic
 
|garlic
 
|Molecular viewer, editor, and visualization program
 
|Molecular viewer, editor, and visualization program
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/garlic/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.zucic.org/garlic/]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/garlic/pkg-descr?revision=HEAD]] [[http://www.zucic.org/garlic/]]
 
|-
 
|-
 
|gperiodic
 
|gperiodic
 
|Displays a periodic table of the elements
 
|Displays a periodic table of the elements
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/gperiodic/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.frantz.fi/software/gperiodic.php]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/gperiodic/pkg-descr?revision=HEAD]] [[http://www.frantz.fi/software/gperiodic.php]]
 
|-
 
|-
 
|haplohseq
 
|haplohseq
 
|Identify regions of allelic imbalance
 
|Identify regions of allelic imbalance
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/haplohseq/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://sites.google.com/site/integrativecancergenomics/software/haplohseq]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/haplohseq/pkg-descr?revision=HEAD]] [[https://sites.google.com/site/integrativecancergenomics/software/haplohseq]]
 
|-
 
|-
 
|hhsuite
 
|hhsuite
 
|Remote protein homology detection suite
 
|Remote protein homology detection suite
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/hhsuite/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/soedinglab/hh-suite]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/hhsuite/pkg-descr?revision=HEAD]] [[https://github.com/soedinglab/hh-suite]]
 
|-
 
|-
 
|igv
 
|igv
 
|Visualization tool for genomic datasets
 
|Visualization tool for genomic datasets
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/igv/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://software.broadinstitute.org/software/igv/]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/igv/pkg-descr?revision=HEAD]] [[https://software.broadinstitute.org/software/igv/]]
 
|-
 
|-
 
|jalview
 
|jalview
 
|Viewer and editor for multiple sequence alignments
 
|Viewer and editor for multiple sequence alignments
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/jalview/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.jalview.org]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/jalview/pkg-descr?revision=HEAD]] [[http://www.jalview.org]]
 
|-
 
|-
 
|kallisto
 
|kallisto
 
|Quantify abundances of transcripts from RNA-Seq data
 
|Quantify abundances of transcripts from RNA-Seq data
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/kallisto/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://pachterlab.github.io/kallisto/about.html]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/kallisto/pkg-descr?revision=HEAD]] [[https://pachterlab.github.io/kallisto/about.html]]
 
|-
 
|-
 
|libghemical
 
|libghemical
Line 112: Line 112:
 
|mafft
 
|mafft
 
|Multiple alignment program for amino acid or nucleotide sequences
 
|Multiple alignment program for amino acid or nucleotide sequences
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/mafft/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://mafft.cbrc.jp/alignment/software/]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/mafft/pkg-descr?revision=HEAD]] [[http://mafft.cbrc.jp/alignment/software/]]
 
|-
 
|-
 
|massxpert
 
|massxpert
Line 120: Line 120:
 
|minc2
 
|minc2
 
|Medical Imaging NetCDF
 
|Medical Imaging NetCDF
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/minc2/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC]]
+
|[[https://svnweb.freebsd.org/ports/head/science/minc2/pkg-descr?revision=HEAD]] [[http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC]]
 
|-
 
|-
 
|molden
 
|molden
 
|Display molecular orbitals and electron densities in 2D and 3D
 
|Display molecular orbitals and electron densities in 2D and 3D
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/molden/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.cmbi.ru.nl/molden/]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/molden/pkg-descr?revision=HEAD]] [[http://www.cmbi.ru.nl/molden/]]
 
|-
 
|-
 
|mmtf-cpp
 
|mmtf-cpp
Line 132: Line 132:
 
|ncbi-blast
 
|ncbi-blast
 
|NCBI implementation of Basic Local Alignment Search Tool
 
|NCBI implementation of Basic Local Alignment Search Tool
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/ncbi-blast+/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://blast.ncbi.nlm.nih.gov]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/ncbi-blast+/pkg-descr?revision=HEAD]] [[http://blast.ncbi.nlm.nih.gov]]
 
|-
 
|-
 
|namd
 
|namd
Line 140: Line 140:
 
|ncbi-cxx-toolkit-
 
|ncbi-cxx-toolkit-
 
|NCBI C++ Toolkit
 
|NCBI C++ Toolkit
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/ncbi-cxx-toolkit/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/ncbi-cxx-toolkit/pkg-descr?revision=HEAD]] [[https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/]]
 
|-
 
|-
 
|p5-Bio-ASN1-EntrezGene
 
|p5-Bio-ASN1-EntrezGene
 
|Regular expression-based Perl Parser for NCBI Entrez Gene
 
|Regular expression-based Perl Parser for NCBI Entrez Gene
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-Bio-ASN1-EntrezGene/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-ASN1-EntrezGene]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-ASN1-EntrezGene/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-ASN1-EntrezGene]]
 
|-
 
|-
 
|p5-Bio-Cluster
 
|p5-Bio-Cluster
 
|BioPerl cluster modules
 
|BioPerl cluster modules
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Cluster/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-Cluster]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Cluster/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Cluster]]
 
|-
 
|-
 
|p5-Bio-Coordinate
 
|p5-Bio-Coordinate
 
|Modules for working with biological coordinates
 
|Modules for working with biological coordinates
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Coordinate/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-Coordinate]]
+
|[[ttps://svnweb.freebsd.org/ports/head/biology/p5-Bio-Coordinate/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Coordinate]]
 
|-
 
|-
 
|p5-Bio-DB-EMBL
 
|p5-Bio-DB-EMBL
 
|Database object interface for EMBL entry retrieval
 
|Database object interface for EMBL entry retrieval
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-Bio-DB-EMBL/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-DB-EMBL]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-DB-EMBL/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-DB-EMBL]]
 
|-
 
|-
 
|p5-Bio-DB-NCBIHelper
 
|p5-Bio-DB-NCBIHelper
 
|Collection of routines useful for queries to NCBI databases
 
|Collection of routines useful for queries to NCBI databases
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-Bio-DB-NCBIHelper/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-DB-NCBIHelper]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-DB-NCBIHelper/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-DB-NCBIHelper]]
 
|-
 
|-
 
|p5-Bio-Das
 
|p5-Bio-Das
 
|Client-side library for Distributed Genome Annotation System
 
|Client-side library for Distributed Genome Annotation System
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Das/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-Das]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Das/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Das]]
 
|-
 
|-
 
|p5-Bio-Das-Lite
 
|p5-Bio-Das-Lite
 
|Perl extension for the DAS (HTTP+XML) Protocol
 
|Perl extension for the DAS (HTTP+XML) Protocol
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Das-Lite/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-Das-Lite]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Das-Lite/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Das-Lite]]
 
|-
 
|-
 
|p5-Bio-FeatureIO
 
|p5-Bio-FeatureIO
 
|Handler for FeatureIO
 
|Handler for FeatureIO
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-Bio-FeatureIO/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-FeatureIO]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-FeatureIO/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-FeatureIO]]
 
|-
 
|-
 
|p5-Bio-GFF3
 
|p5-Bio-GFF3
 
|Fast low-level functions for parsing and formatting GFF3
 
|Fast low-level functions for parsing and formatting GFF3
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-Bio-GFF3/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-GFF3]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-GFF3/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-GFF3]]
 
|-
 
|-
 
|p5-Bio-Glite
 
|p5-Bio-Glite
 
|Perl Interface to G-language
 
|Perl Interface to G-language
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Glite/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-Glite]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Glite/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Glite]]
 
|-
 
|-
 
|p5-Bio-Graphics
 
|p5-Bio-Graphics
 
|Generate GD Images of Bio::Seq Objects
 
|Generate GD Images of Bio::Seq Objects
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Graphics/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-Graphics]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Graphics/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Graphics]]
 
|-
 
|-
 
|p5-Bio-MAGETAB
 
|p5-Bio-MAGETAB
 
|Data model and utility API for the MAGE-TAB format
 
|Data model and utility API for the MAGE-TAB format
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-Bio-MAGETAB/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-MAGETAB]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-MAGETAB/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-MAGETAB]]
 
|-
 
|-
 
|p5-Bio-NEXUS
 
|p5-Bio-NEXUS
 
|Object-oriented Perl API for the NEXUS file format
 
|Object-oriented Perl API for the NEXUS file format
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-Bio-NEXUS/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-NEXUS]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-NEXUS/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-NEXUS]]
 
|-
 
|-
 
|p5-Bio-Phylo
 
|p5-Bio-Phylo
 
|Phylogenetic analysis using Perl
 
|Phylogenetic analysis using Perl
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Phylo/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-Phylo]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Phylo/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Phylo]]
 
|-
 
|-
 
|p5-Bio-SCF
 
|p5-Bio-SCF
 
|Read and Update SCF Chromatographic Sequence Files
 
|Read and Update SCF Chromatographic Sequence Files
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-Bio-SCF/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-SCF]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-SCF/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-SCF]]
 
|-
 
|-
 
|p5-Bio-Variation
 
|p5-Bio-Variation
 
|BioPerl variation-related functionality
 
|BioPerl variation-related functionality
−
|[[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-Variation]]
+
|[[https://metacpan.org/release/Bio-Variation]]
 
|-
 
|-
 
|p5-BioPerl
 
|p5-BioPerl
 
|Collection of Perl modules for bioinformatics
 
|Collection of Perl modules for bioinformatics
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-BioPerl/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://bioperl.org/]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-BioPerl/pkg-descr?revision=HEAD]] [[https://bioperl.org/]]
 
|-
 
|-
 
|p5-BioPerl-Run
 
|p5-BioPerl-Run
 
|Wrapper modules for common bioinformatics tools
 
|Wrapper modules for common bioinformatics tools
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-BioPerl-Run/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/bioperl/bioperl-run]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-BioPerl-Run/pkg-descr?revision=HEAD]] [[https://github.com/bioperl/bioperl-run]]
 
|-
 
|-
 
|p5-TrimGalore
 
|p5-TrimGalore
 
|Wrapper around Cutadapt and FastQC for adapter and quality trimming
 
|Wrapper around Cutadapt and FastQC for adapter and quality trimming
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/p5-TrimGalore/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/FelixKrueger/TrimGalore]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/p5-TrimGalore/pkg-descr?revision=HEAD]] [[https://github.com/FelixKrueger/TrimGalore]]
 
|-
 
|-
 
|pbcopper
 
|pbcopper
 
|Core C++ library for Pacific Biosciences tools
 
|Core C++ library for Pacific Biosciences tools
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/pbcopper/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/PacificBiosciences/pbcopper]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/pbcopper/pkg-descr?revision=HEAD]] [[https://github.com/PacificBiosciences/pbcopper]]
 
|-
 
|-
 
|plinkseq
 
|plinkseq
Line 228: Line 228:
 
|prodigal
 
|prodigal
 
|Protein-coding gene prediction for prokaryotic genomes
 
|Protein-coding gene prediction for prokaryotic genomes
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/prodigal/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/hyattpd/Prodigal]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/prodigal/pkg-descr?revision=HEAD]] [[https://github.com/hyattpd/Prodigal]]
 
|-
 
|-
 
|py27-multiqc
 
|py27-multiqc
 
|Aggregate bioinformatics analysis reports across samples and tools
 
|Aggregate bioinformatics analysis reports across samples and tools
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/py-multiqc/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://pypi.python.org/pypi/multiqc]]
+
|[[https://svnweb.freebsd.org/ports/head/biology/py-multiqc/pkg-descr?revision=HEAD]] [[https://pypi.python.org/pypi/multiqc]]
 
|-
 
|-
 
|py27-pymol
 
|py27-pymol
 
|OpenGL-based molecular visualization system
 
|OpenGL-based molecular visualization system
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-pymol/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://pymol.org/2/]]
+
|[[https://svnweb.freebsd.org/ports/head/science/py-pymol/pkg-descr?revision=HEAD]] [[https://pymol.org/2/]]
 
|-
 
|-
 
|py37-chainer-chemistry
 
|py37-chainer-chemistry
 
|Library for deep learning in biology and chemistry
 
|Library for deep learning in biology and chemistry
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/py-chainer-chemistry/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/pfnet-research/chainer-chemistry]]
+
|[[https://svnweb.freebsd.org/ports/head/science/py-chainer-chemistry/pkg-descr?revision=HEAD]] [[https://github.com/pfnet-research/chainer-chemistry]]
 
|-
 
|-
−
|py37-multiqc
+
|
−
|Aggregate bioinformatics analysis reports across samples and tools
+
|[[]] [[]]
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/py-multiqc/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://pypi.python.org/pypi/multiqc]]
+
|-
 +
|
 +
|[[]] [[]]
 +
|-
 +
|
 +
|[[]] [[]]
 
|-
 
|-
−
|py37-orange3-bioinformatics
+
|
−
|Orange add-on providing common functionality for bioinformatics
+
|[[]] [[]]
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/py-orange3-bioinformatics/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/biolab/orange3-bioinformatics]]
+
 
|-
 
|-
−
|py37-orange3-single-cell
+
|
−
|Orange add-on for gene expression of single cell data
+
|[[]] [[]]
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/py-orange3-single-cell/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://singlecell.biolab.si/]]
+
 
|-
 
|-
−
|pycogent
+
|
−
|Toolkit for statistical analysis of biological sequences
+
|[[]] [[]]
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/pycogent/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://pycogent.sourceforge.net/]]
+
 
|-
 
|-
−
|raster3d
+
|
−
|Set of tools for generating raster images of proteins and molecules
+
|[[]] [[]]
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/graphics/raster3d/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://skuld.bmsc.washington.edu/raster3d/]]
+
 
|-
 
|-
−
|seqtools
+
|
−
|Tools for visualising sequence alignments
+
|[[]] [[]]
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/seqtools/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.sanger.ac.uk/science/tools/seqtools]]
+
 
|-
 
|-
−
|ugene
+
|
−
|Free, open-source, cross-platform bioinformatics toolkit
+
|[[]] [[]]
−
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/ugene/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://ugene.unipro.ru/]]
+
 
|-
 
|-
 
!colspan="3"|
 
!colspan="3"|
 
|-
 
|-
−
!colspan="3"|'''If you don't find a package, you are looking for, <br/>we recommend to search the ''' [[File:Icon FreeBSD.png|50px|link=https://www.freebsd.org/ports/categories-grouped.html]]'''Ports Collection. If it is there, than it is also in the GhostBSD ports. '''
+
!colspan="3"|'''If you don't find a package, you are looking for, <br/>we recommend to search the ''' [[File:Icon FreeBSD.png|50px|link=https://www.freebsd.org/ports/categories-grouped.html]]'''Ports Collection.'''
 
|-
 
|-
 
!colspan="3"|
 
!colspan="3"|

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