Editing Biology

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|style="text-align:center;padding: 10px" | '''Welcome to the'''[[image:Icon Disti GhostBSD.png|100px|link=http://www.ghostbsd.org/]] '''{{PAGENAME}}'''
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! scope="col" style="width: 100px;"|'''App/Package'''
! scope="col" style="width: 350px;"|'''Abstract'''
! scope="col" style="width: 250px;"|'''Addition or Link'''
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|CheckM
|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/]]
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|GroopM
|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/]]
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|InsightToolkit
|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]]
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|Jellyfish
|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]]
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|abyss
|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/]]
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|afni
|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/]]
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|artemis
|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]]
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|avida
|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/]]
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|babel
|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/]]
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|bamtools
|API and toolkit for handling BAM files
|[[File:1329059652.png|35px|link=https://github.com/pezmaster31/bamtools]]
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|biococoa
|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/]]
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|canu
|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/]]
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|cycle
|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/]]
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|cytoscape
|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]]
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|dDocent
|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]]
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|emboss
|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/]]
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|figtree
|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/]]
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|garlic
|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/]]
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|gperiodic
|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]]
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|haplohseq
|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]]
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|hhsuite
|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]]
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|igv
|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/]]
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|jalview
|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]]
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|kallisto
|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]]
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|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]] 
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|mafft
|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/]]
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|minc2
|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]]
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|molden
|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/]]
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|ncbi-blast
|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]]
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|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/]]
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|ncbi-cxx-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/]]
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|p5-Bio-ASN1-EntrezGene
|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]]
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|p5-Bio-Cluster
|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]]
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|p5-Bio-Coordinate
|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]]
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|p5-Bio-DB-EMBL
|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]]
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|p5-Bio-DB-NCBIHelper
|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]]
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|p5-Bio-Das
|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]]
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|p5-Bio-Das-Lite
|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]]
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|p5-Bio-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]]
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|p5-Bio-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]]
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|p5-Bio-Glite
|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]]
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|p5-Bio-Graphics
|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]]
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|p5-Bio-MAGETAB
|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]]
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|p5-Bio-NEXUS
|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]]
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|p5-Bio-Phylo
|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]]
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|p5-Bio-SCF
|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]]
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|p5-Bio-Variation
|BioPerl variation-related functionality
|[[File:1329059652.png|35px|link=https://metacpan.org/release/Bio-Variation]]
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|p5-BioPerl
|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/]]
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|p5-BioPerl-Run
|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]]
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|p5-TrimGalore
|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]]
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|pbcopper
|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]]
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|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/]]
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|prodigal
|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]]
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|py27-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]]
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|py27-pymol
|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/]]
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|py37-chainer-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]]
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|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]]
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|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]]
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|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/]]
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|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/]]
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|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/]]
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|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]]
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|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/]]
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!colspan="3"|
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!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. '''
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!colspan="3"|
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!colspan="3"|'''Back to ''' [[image:Icon Disti GhostBSD.png|50px|link=Science and Engineering]] '''Science and Engineering'''
|}


[[Category:Station]]
@@ Line 113: / Line 113: @@
 |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/]]
-|-
-|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
@@ Line 125: / Line 121: @@
 |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/]]
-|-
-|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