Difference between revisions of "Biology"

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|CheckM
 
|CheckM
 
|Quality assessment tool for the microbial genomes
 
|Quality assessment tool for the microbial genomes
−
|[[https://svnweb.freebsd.org/ports/head/biology/checkm/pkg-descr?revision=HEAD]] [[https://ecogenomics.github.io/CheckM/]]
+
|[[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/]]
 
|-
 
|-
 
|GroopM
 
|GroopM
 
|Metagenomic binning suite
 
|Metagenomic binning suite
−
|[[https://svnweb.freebsd.org/ports/head/biology/groopm/pkg-descr?revision=HEAD]] [[http://ecogenomics.github.io/GroopM/]]
+
|[[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/]]
 
|-
 
|-
 
|InsightToolkit
 
|InsightToolkit
 
|Insight Toolkit
 
|Insight Toolkit
−
|[[https://svnweb.freebsd.org/ports/head/science/InsightToolkit/pkg-descr?revision=HEAD]] [[http://www.itk.org]]
+
|[[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]]
 
|-
 
|-
 
|Jellyfish
 
|Jellyfish
 
|Fast, memory-efficient counting of k-mers in DNA
 
|Fast, memory-efficient counting of k-mers in DNA
−
|[[https://svnweb.freebsd.org/ports/head/biology/jellyfish/pkg-descr?revision=HEAD]] [[http://www.genome.umd.edu/jellyfish.html]]
+
|[[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]]
 
|-
 
|-
 
|abyss
 
|abyss
 
|Assembly By Short Sequences: parallel, paired-end sequence assembler
 
|Assembly By Short Sequences: parallel, paired-end sequence assembler
−
|[[https://svnweb.freebsd.org/ports/head/science/afni/pkg-descr?revision=HEAD]] [[http://afni.nimh.nih.gov/afni/]]
+
|[[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/]]
 
|-
 
|-
 
|afni
 
|afni
 
|Advanced Functional Neuro Imaging
 
|Advanced Functional Neuro Imaging
−
|[[https://svnweb.freebsd.org/ports/head/science/afni/pkg-descr?revision=HEAD]] [[http://afni.nimh.nih.gov/afni/]]
+
|[[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/]]
 
|-
 
|-
 
|artemis
 
|artemis
 
|DNA sequence viewer and annotation tool
 
|DNA sequence viewer and annotation tool
−
|[[https://svnweb.freebsd.org/ports/head/biology/artemis/pkg-descr?revision=HEAD]] [[https://www.sanger.ac.uk/science/tools/artemis]]
+
|[[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]]
 
|-
 
|-
 
|avida
 
|avida
 
|Auto-adaptive genetic system designed for ALife research
 
|Auto-adaptive genetic system designed for ALife research
−
|[[https://svnweb.freebsd.org/ports/head/biology/avida/pkg-descr?revision=HEAD]] [[http://avida.devosoft.org/]]
+
|[[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/]]
 
|-
 
|-
 
|babel
 
|babel
 
|Converts among various molecular file formats
 
|Converts among various molecular file formats
−
|[[https://svnweb.freebsd.org/ports/head/biology/babel/pkg-descr?revision=HEAD]] [[http://smog.com/chem/babel/]]
+
|[[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/]]
 
|-
 
|-
 
|bamtools
 
|bamtools
 
|API and toolkit for handling BAM files
 
|API and toolkit for handling BAM files
−
|[[https://github.com/pezmaster31/bamtools]]
+
|[[File:1329059652.png|35px|link=https://github.com/pezmaster31/bamtools]]
 
|-
 
|-
 
|biococoa
 
|biococoa
 
|Bioinformatics framework
 
|Bioinformatics framework
−
|[[https://svnweb.freebsd.org/ports/head/biology/biococoa/pkg-descr?revision=HEAD]] [[http://bioinformatics.org/biococoa/]]
+
|[[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/]]
 
|-
 
|-
 
|canu
 
|canu
 
|Single molecule sequence assembler
 
|Single molecule sequence assembler
−
|[[https://svnweb.freebsd.org/ports/head/biology/canu/pkg-descr?revision=HEAD]] [[https://canu.readthedocs.io/]]
+
|[[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/]]
 
|-
 
|-
 
|cycle
 
|cycle
 
|Calendar program for women
 
|Calendar program for women
−
|[[https://svnweb.freebsd.org/ports/head/deskutils/cycle/pkg-descr?revision=HEAD]] [[http://cycle.sourceforge.net/]]
+
|[[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/]]
 
|-
 
|-
 
|cytoscape
 
|cytoscape
 
|Software to visualize molecular interaction networks, gene expression
 
|Software to visualize molecular interaction networks, gene expression
−
|[[https://svnweb.freebsd.org/ports/head/biology/cytoscape/pkg-descr?revision=HEAD]] [[http://www.cytoscape.org]]
+
|[[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]]
 
|-
 
|-
 
|dDocent
 
|dDocent
 
|Bash pipeline for RAD sequencing
 
|Bash pipeline for RAD sequencing
−
|[[https://svnweb.freebsd.org/ports/head/biology/ddocent/pkg-descr?revision=HEAD]] [[http://ddocent.com]]
+
|[[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]]
 
|-
 
|-
 
|emboss
 
|emboss
 
|Collection of open source tools for genetic sequence analysis
 
|Collection of open source tools for genetic sequence analysis
−
|[[https://svnweb.freebsd.org/ports/head/biology/emboss/pkg-descr?revision=HEAD]] [[http://www.emboss.org/]]
+
|[[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/]]
 
|-
 
|-
 
|figtree
 
|figtree
 
|Graphical viewer of phylogenetic trees
 
|Graphical viewer of phylogenetic trees
−
|[[https://svnweb.freebsd.org/ports/head/biology/figtree/pkg-descr?revision=HEAD]] [[http://tree.bio.ed.ac.uk/software/figtree/]]
+
|[[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/]]
 
|-
 
|-
 
|garlic
 
|garlic
 
|Molecular viewer, editor, and visualization program
 
|Molecular viewer, editor, and visualization program
−
|[[https://svnweb.freebsd.org/ports/head/biology/garlic/pkg-descr?revision=HEAD]] [[http://www.zucic.org/garlic/]]
+
|[[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/]]
 
|-
 
|-
 
|gperiodic
 
|gperiodic
 
|Displays a periodic table of the elements
 
|Displays a periodic table of the elements
−
|[[https://svnweb.freebsd.org/ports/head/biology/gperiodic/pkg-descr?revision=HEAD]] [[http://www.frantz.fi/software/gperiodic.php]]
+
|[[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]]
 
|-
 
|-
 
|haplohseq
 
|haplohseq
 
|Identify regions of allelic imbalance
 
|Identify regions of allelic imbalance
−
|[[https://svnweb.freebsd.org/ports/head/biology/haplohseq/pkg-descr?revision=HEAD]] [[https://sites.google.com/site/integrativecancergenomics/software/haplohseq]]
+
|[[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]]
 
|-
 
|-
 
|hhsuite
 
|hhsuite
 
|Remote protein homology detection suite
 
|Remote protein homology detection suite
−
|[[https://svnweb.freebsd.org/ports/head/biology/hhsuite/pkg-descr?revision=HEAD]] [[https://github.com/soedinglab/hh-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]]
 
|-
 
|-
 
|igv
 
|igv
 
|Visualization tool for genomic datasets
 
|Visualization tool for genomic datasets
−
|[[https://svnweb.freebsd.org/ports/head/biology/igv/pkg-descr?revision=HEAD]] [[https://software.broadinstitute.org/software/igv/]]
+
|[[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/]]
 
|-
 
|-
 
|jalview
 
|jalview
 
|Viewer and editor for multiple sequence alignments
 
|Viewer and editor for multiple sequence alignments
−
|[[https://svnweb.freebsd.org/ports/head/biology/jalview/pkg-descr?revision=HEAD]] [[http://www.jalview.org]]
+
|[[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]]
 
|-
 
|-
 
|kallisto
 
|kallisto
 
|Quantify abundances of transcripts from RNA-Seq data
 
|Quantify abundances of transcripts from RNA-Seq data
−
|[[https://svnweb.freebsd.org/ports/head/biology/kallisto/pkg-descr?revision=HEAD]] [[https://pachterlab.github.io/kallisto/about.html]]
+
|[[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]]
 +
|-
 +
|libghemical
 +
|Support libraries of science/ghemical port
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/libghemical/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.bioinformatics.org/ghemical/ghemical/index.html]]  
 
|-
 
|-
 
|mafft
 
|mafft
 
|Multiple alignment program for amino acid or nucleotide sequences
 
|Multiple alignment program for amino acid or nucleotide sequences
−
|[[https://svnweb.freebsd.org/ports/head/biology/mafft/pkg-descr?revision=HEAD]] [[http://mafft.cbrc.jp/alignment/software/]]
+
|[[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/]]
 +
|-
 +
|massxpert
 +
|massXpert software for (bio)chemists
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/massxpert/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://salsa.debian.org/debichem-team/massxpert]]
 
|-
 
|-
 
|minc2
 
|minc2
 
|Medical Imaging NetCDF
 
|Medical Imaging NetCDF
−
|[[https://svnweb.freebsd.org/ports/head/science/minc2/pkg-descr?revision=HEAD]] [[http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC]]
+
|[[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]]
 
|-
 
|-
 
|molden
 
|molden
 
|Display molecular orbitals and electron densities in 2D and 3D
 
|Display molecular orbitals and electron densities in 2D and 3D
−
|[[https://svnweb.freebsd.org/ports/head/biology/molden/pkg-descr?revision=HEAD]] [[http://www.cmbi.ru.nl/molden/]]
+
|[[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/]]
 +
|-
 +
|mmtf-cpp
 +
|C++ MMTF format API, decoder and encoder, for molecular structures
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/mmtf-cpp/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://mmtf.rcsb.org/]]  
 
|-
 
|-
 
|ncbi-blast
 
|ncbi-blast
 
|NCBI implementation of Basic Local Alignment Search Tool
 
|NCBI implementation of Basic Local Alignment Search Tool
−
|[[https://svnweb.freebsd.org/ports/head/biology/ncbi-blast+/pkg-descr?revision=HEAD]] [[http://blast.ncbi.nlm.nih.gov]]
+
|[[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]]
 +
|-
 +
|namd
 +
|Computer software for molecular dynamics simulation
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/namd/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.ks.uiuc.edu/Research/namd/]]
 
|-
 
|-
 
|ncbi-cxx-toolkit-
 
|ncbi-cxx-toolkit-
 
|NCBI C++ Toolkit
 
|NCBI C++ Toolkit
−
|[[https://svnweb.freebsd.org/ports/head/biology/ncbi-cxx-toolkit/pkg-descr?revision=HEAD]] [[https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/]]
+
|[[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/]]
 
|-
 
|-
 
|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
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-ASN1-EntrezGene/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-ASN1-EntrezGene]]
+
|[[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]]
 
|-
 
|-
 
|p5-Bio-Cluster
 
|p5-Bio-Cluster
 
|BioPerl cluster modules
 
|BioPerl cluster modules
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Cluster/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Cluster]]
+
|[[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]]
 
|-
 
|-
 
|p5-Bio-Coordinate
 
|p5-Bio-Coordinate
 
|Modules for working with biological coordinates
 
|Modules for working with biological coordinates
−
|[[ttps://svnweb.freebsd.org/ports/head/biology/p5-Bio-Coordinate/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Coordinate]]
+
|[[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]]
 
|-
 
|-
 
|p5-Bio-DB-EMBL
 
|p5-Bio-DB-EMBL
 
|Database object interface for EMBL entry retrieval
 
|Database object interface for EMBL entry retrieval
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-DB-EMBL/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-DB-EMBL]]
+
|[[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]]
 
|-
 
|-
 
|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
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-DB-NCBIHelper/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-DB-NCBIHelper]]
+
|[[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]]
 
|-
 
|-
 
|p5-Bio-Das
 
|p5-Bio-Das
 
|Client-side library for Distributed Genome Annotation System
 
|Client-side library for Distributed Genome Annotation System
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Das/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Das]]
+
|[[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]]
 
|-
 
|-
 
|p5-Bio-Das-Lite
 
|p5-Bio-Das-Lite
 
|Perl extension for the DAS (HTTP+XML) Protocol
 
|Perl extension for the DAS (HTTP+XML) Protocol
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Das-Lite/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Das-Lite]]
+
|[[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]]
 
|-
 
|-
 
|p5-Bio-FeatureIO
 
|p5-Bio-FeatureIO
 
|Handler for FeatureIO
 
|Handler for FeatureIO
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-FeatureIO/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-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]]
 
|-
 
|-
 
|p5-Bio-GFF3
 
|p5-Bio-GFF3
 
|Fast low-level functions for parsing and formatting GFF3
 
|Fast low-level functions for parsing and formatting GFF3
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-GFF3/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-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]]
 
|-
 
|-
 
|p5-Bio-Glite
 
|p5-Bio-Glite
 
|Perl Interface to G-language
 
|Perl Interface to G-language
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Glite/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Glite]]
+
|[[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]]
 
|-
 
|-
 
|p5-Bio-Graphics
 
|p5-Bio-Graphics
 
|Generate GD Images of Bio::Seq Objects
 
|Generate GD Images of Bio::Seq Objects
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Graphics/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Graphics]]
+
|[[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]]
 
|-
 
|-
 
|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
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-MAGETAB/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-MAGETAB]]
+
|[[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]]
 
|-
 
|-
 
|p5-Bio-NEXUS
 
|p5-Bio-NEXUS
 
|Object-oriented Perl API for the NEXUS file format
 
|Object-oriented Perl API for the NEXUS file format
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-NEXUS/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-NEXUS]]
+
|[[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]]
 
|-
 
|-
 
|p5-Bio-Phylo
 
|p5-Bio-Phylo
 
|Phylogenetic analysis using Perl
 
|Phylogenetic analysis using Perl
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Phylo/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Phylo]]
+
|[[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]]
 
|-
 
|-
 
|p5-Bio-SCF
 
|p5-Bio-SCF
 
|Read and Update SCF Chromatographic Sequence Files
 
|Read and Update SCF Chromatographic Sequence Files
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-SCF/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-SCF]]
+
|[[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]]
 
|-
 
|-
 
|p5-Bio-Variation
 
|p5-Bio-Variation
 
|BioPerl variation-related functionality
 
|BioPerl variation-related functionality
−
|[[https://metacpan.org/release/Bio-Variation]]
+
|[[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-Variation]]
 
|-
 
|-
 
|p5-BioPerl
 
|p5-BioPerl
 
|Collection of Perl modules for bioinformatics
 
|Collection of Perl modules for bioinformatics
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-BioPerl/pkg-descr?revision=HEAD]] [[https://bioperl.org/]]
+
|[[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/]]
 
|-
 
|-
 
|p5-BioPerl-Run
 
|p5-BioPerl-Run
 
|Wrapper modules for common bioinformatics tools
 
|Wrapper modules for common bioinformatics tools
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-BioPerl-Run/pkg-descr?revision=HEAD]] [[https://github.com/bioperl/bioperl-run]]
+
|[[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]]
 
|-
 
|-
 
|p5-TrimGalore
 
|p5-TrimGalore
 
|Wrapper around Cutadapt and FastQC for adapter and quality trimming
 
|Wrapper around Cutadapt and FastQC for adapter and quality trimming
−
|[[https://svnweb.freebsd.org/ports/head/biology/p5-TrimGalore/pkg-descr?revision=HEAD]] [[https://github.com/FelixKrueger/TrimGalore]]
+
|[[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]]
 
|-
 
|-
 
|pbcopper
 
|pbcopper
 
|Core C++ library for Pacific Biosciences tools
 
|Core C++ library for Pacific Biosciences tools
−
|[[https://svnweb.freebsd.org/ports/head/biology/pbcopper/pkg-descr?revision=HEAD]] [[https://github.com/PacificBiosciences/pbcopper]]
+
|[[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]]
 +
|-
 +
|plinkseq
 +
|Toolset for working with human genetic variation data
 +
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/plinkseq/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://atgu.mgh.harvard.edu/plinkseq/]]
 
|-
 
|-
 
|prodigal
 
|prodigal
 
|Protein-coding gene prediction for prokaryotic genomes
 
|Protein-coding gene prediction for prokaryotic genomes
−
|[[https://svnweb.freebsd.org/ports/head/biology/prodigal/pkg-descr?revision=HEAD]] [[https://github.com/hyattpd/Prodigal]]
+
|[[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]]
 
|-
 
|-
 
|py27-multiqc
 
|py27-multiqc
 
|Aggregate bioinformatics analysis reports across samples and tools
 
|Aggregate bioinformatics analysis reports across samples and tools
−
|[[https://svnweb.freebsd.org/ports/head/biology/py-multiqc/pkg-descr?revision=HEAD]] [[https://pypi.python.org/pypi/multiqc]]
+
|[[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]]
 
|-
 
|-
 
|py27-pymol
 
|py27-pymol
 
|OpenGL-based molecular visualization system
 
|OpenGL-based molecular visualization system
−
|[[https://svnweb.freebsd.org/ports/head/science/py-pymol/pkg-descr?revision=HEAD]] [[https://pymol.org/2/]]
+
|[[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/]]
 
|-
 
|-
 
|py37-chainer-chemistry
 
|py37-chainer-chemistry
 
|Library for deep learning in biology and chemistry
 
|Library for deep learning in biology and chemistry
−
|[[https://svnweb.freebsd.org/ports/head/science/py-chainer-chemistry/pkg-descr?revision=HEAD]] [[https://github.com/pfnet-research/chainer-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]]
 
|-
 
|-
−
|
+
|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.'''
+
!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"|
 
!colspan="3"|
 
|-
 
|-
−
!colspan="3"|'''Back to the''' [[image:Icon Disti GhostBSD.png|50px|link=Office Applications]]'''Office Applications'''
+
!colspan="3"|'''Back to ''' [[image:Icon Disti GhostBSD.png|50px|link=Science and Engineering]] '''Science and Engineering'''
−
 
+
 
|}
 
|}
  
  
 
[[Category:Station]]
 
[[Category:Station]]

Latest revision as of 13:19, 20 January 2020

Welcome to theIcon Disti GhostBSD.png Biology
App/Package Abstract Addition or Link
CheckM Quality assessment tool for the microbial genomes Icon FreeBSD.png 1329059652.png
GroopM Metagenomic binning suite Icon FreeBSD.png 1329059652.png
InsightToolkit Insight Toolkit Icon FreeBSD.png 1329059652.png
Jellyfish Fast, memory-efficient counting of k-mers in DNA Icon FreeBSD.png 1329059652.png
abyss Assembly By Short Sequences: parallel, paired-end sequence assembler Icon FreeBSD.png 1329059652.png
afni Advanced Functional Neuro Imaging Icon FreeBSD.png 1329059652.png
artemis DNA sequence viewer and annotation tool Icon FreeBSD.png 1329059652.png
avida Auto-adaptive genetic system designed for ALife research Icon FreeBSD.png 1329059652.png
babel Converts among various molecular file formats Icon FreeBSD.png 1329059652.png
bamtools API and toolkit for handling BAM files 1329059652.png
biococoa Bioinformatics framework Icon FreeBSD.png 1329059652.png
canu Single molecule sequence assembler Icon FreeBSD.png 1329059652.png
cycle Calendar program for women Icon FreeBSD.png 1329059652.png
cytoscape Software to visualize molecular interaction networks, gene expression Icon FreeBSD.png 1329059652.png
dDocent Bash pipeline for RAD sequencing Icon FreeBSD.png 1329059652.png
emboss Collection of open source tools for genetic sequence analysis Icon FreeBSD.png 1329059652.png
figtree Graphical viewer of phylogenetic trees Icon FreeBSD.png 1329059652.png
garlic Molecular viewer, editor, and visualization program Icon FreeBSD.png 1329059652.png
gperiodic Displays a periodic table of the elements Icon FreeBSD.png 1329059652.png
haplohseq Identify regions of allelic imbalance Icon FreeBSD.png 1329059652.png
hhsuite Remote protein homology detection suite Icon FreeBSD.png 1329059652.png
igv Visualization tool for genomic datasets Icon FreeBSD.png 1329059652.png
jalview Viewer and editor for multiple sequence alignments Icon FreeBSD.png 1329059652.png
kallisto Quantify abundances of transcripts from RNA-Seq data Icon FreeBSD.png 1329059652.png
libghemical Support libraries of science/ghemical port Icon FreeBSD.png 1329059652.png
mafft Multiple alignment program for amino acid or nucleotide sequences Icon FreeBSD.png 1329059652.png
massxpert massXpert software for (bio)chemists Icon FreeBSD.png 1329059652.png
minc2 Medical Imaging NetCDF Icon FreeBSD.png 1329059652.png
molden Display molecular orbitals and electron densities in 2D and 3D Icon FreeBSD.png 1329059652.png
mmtf-cpp C++ MMTF format API, decoder and encoder, for molecular structures Icon FreeBSD.png 1329059652.png
ncbi-blast NCBI implementation of Basic Local Alignment Search Tool Icon FreeBSD.png 1329059652.png
namd Computer software for molecular dynamics simulation Icon FreeBSD.png 1329059652.png
ncbi-cxx-toolkit- NCBI C++ Toolkit Icon FreeBSD.png 1329059652.png
p5-Bio-ASN1-EntrezGene Regular expression-based Perl Parser for NCBI Entrez Gene Icon FreeBSD.png 1329059652.png
p5-Bio-Cluster BioPerl cluster modules Icon FreeBSD.png 1329059652.png
p5-Bio-Coordinate Modules for working with biological coordinates Icon FreeBSD.png 1329059652.png
p5-Bio-DB-EMBL Database object interface for EMBL entry retrieval Icon FreeBSD.png 1329059652.png
p5-Bio-DB-NCBIHelper Collection of routines useful for queries to NCBI databases Icon FreeBSD.png 1329059652.png
p5-Bio-Das Client-side library for Distributed Genome Annotation System Icon FreeBSD.png 1329059652.png
p5-Bio-Das-Lite Perl extension for the DAS (HTTP+XML) Protocol Icon FreeBSD.png 1329059652.png
p5-Bio-FeatureIO Handler for FeatureIO Icon FreeBSD.png 1329059652.png
p5-Bio-GFF3 Fast low-level functions for parsing and formatting GFF3 Icon FreeBSD.png 1329059652.png
p5-Bio-Glite Perl Interface to G-language Icon FreeBSD.png 1329059652.png
p5-Bio-Graphics Generate GD Images of Bio::Seq Objects Icon FreeBSD.png 1329059652.png
p5-Bio-MAGETAB Data model and utility API for the MAGE-TAB format Icon FreeBSD.png 1329059652.png
p5-Bio-NEXUS Object-oriented Perl API for the NEXUS file format Icon FreeBSD.png 1329059652.png
p5-Bio-Phylo Phylogenetic analysis using Perl Icon FreeBSD.png 1329059652.png
p5-Bio-SCF Read and Update SCF Chromatographic Sequence Files Icon FreeBSD.png 1329059652.png
p5-Bio-Variation BioPerl variation-related functionality 1329059652.png
p5-BioPerl Collection of Perl modules for bioinformatics Icon FreeBSD.png 1329059652.png
p5-BioPerl-Run Wrapper modules for common bioinformatics tools Icon FreeBSD.png 1329059652.png
p5-TrimGalore Wrapper around Cutadapt and FastQC for adapter and quality trimming Icon FreeBSD.png 1329059652.png
pbcopper Core C++ library for Pacific Biosciences tools Icon FreeBSD.png 1329059652.png
plinkseq Toolset for working with human genetic variation data Icon FreeBSD.png 1329059652.png
prodigal Protein-coding gene prediction for prokaryotic genomes Icon FreeBSD.png 1329059652.png
py27-multiqc Aggregate bioinformatics analysis reports across samples and tools Icon FreeBSD.png 1329059652.png
py27-pymol OpenGL-based molecular visualization system Icon FreeBSD.png 1329059652.png
py37-chainer-chemistry Library for deep learning in biology and chemistry Icon FreeBSD.png 1329059652.png
py37-multiqc Aggregate bioinformatics analysis reports across samples and tools Icon FreeBSD.png 1329059652.png
py37-orange3-bioinformatics Orange add-on providing common functionality for bioinformatics Icon FreeBSD.png 1329059652.png
py37-orange3-single-cell Orange add-on for gene expression of single cell data Icon FreeBSD.png 1329059652.png
pycogent Toolkit for statistical analysis of biological sequences Icon FreeBSD.png 1329059652.png
raster3d Set of tools for generating raster images of proteins and molecules Icon FreeBSD.png 1329059652.png
seqtools Tools for visualising sequence alignments Icon FreeBSD.png 1329059652.png
ugene Free, open-source, cross-platform bioinformatics toolkit Icon FreeBSD.png 1329059652.png
If you don't find a package, you are looking for,
we recommend to search the Icon FreeBSD.pngPorts Collection. If it is there, than it is also in the GhostBSD ports.
Back to Icon Disti GhostBSD.png Science and Engineering
Retrieved from "http://wiki.ghostbsd.org/index.php?title=Biology&oldid=3834"