Difference between revisions of "Biology"

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|[[https://svnweb.freebsd.org/ports/head/biology/igv/pkg-descr?revision=HEAD]] [[https://software.broadinstitute.org/software/igv/]]
 
|[[https://svnweb.freebsd.org/ports/head/biology/igv/pkg-descr?revision=HEAD]] [[https://software.broadinstitute.org/software/igv/]]
 
|-
 
|-
−
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+
|jalview
−
|[[]] [[]]
+
|Viewer and editor for multiple sequence alignments
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|[[https://svnweb.freebsd.org/ports/head/biology/jalview/pkg-descr?revision=HEAD]] [[http://www.jalview.org]]
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|-
 +
|kallisto
 +
|Quantify abundances of transcripts from RNA-Seq data
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|[[https://svnweb.freebsd.org/ports/head/biology/kallisto/pkg-descr?revision=HEAD]] [[https://pachterlab.github.io/kallisto/about.html]]
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|-
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|mafft
 +
|Multiple alignment program for amino acid or nucleotide sequences
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|[[https://svnweb.freebsd.org/ports/head/biology/mafft/pkg-descr?revision=HEAD]] [[http://mafft.cbrc.jp/alignment/software/]]
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|-
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|minc2
 +
|Medical Imaging NetCDF
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|[[https://svnweb.freebsd.org/ports/head/science/minc2/pkg-descr?revision=HEAD]] [[http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC]]
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|-
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|molden
 +
|Display molecular orbitals and electron densities in 2D and 3D
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|[[https://svnweb.freebsd.org/ports/head/biology/molden/pkg-descr?revision=HEAD]] [[http://www.cmbi.ru.nl/molden/]]
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|-
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|ncbi-blast
 +
|NCBI implementation of Basic Local Alignment Search Tool
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|[[https://svnweb.freebsd.org/ports/head/biology/ncbi-blast+/pkg-descr?revision=HEAD]] [[http://blast.ncbi.nlm.nih.gov]]
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|-
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|ncbi-cxx-toolkit-
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|NCBI C++ Toolkit
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|[[https://svnweb.freebsd.org/ports/head/biology/ncbi-cxx-toolkit/pkg-descr?revision=HEAD]] [[https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/]]
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|-
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|p5-Bio-ASN1-EntrezGene
 +
|Regular expression-based Perl Parser for NCBI Entrez Gene
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|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-ASN1-EntrezGene/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-ASN1-EntrezGene]]
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|-
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|p5-Bio-Cluster
 +
|BioPerl cluster modules
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|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Cluster/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Cluster]]
 +
|-
 +
|p5-Bio-Coordinate
 +
|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]]
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|-
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|p5-Bio-DB-EMBL
 +
|Database object interface for EMBL entry retrieval
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|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-DB-EMBL/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-DB-EMBL]]
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|-
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|p5-Bio-DB-NCBIHelper
 +
|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]]
 +
|-
 +
|p5-Bio-Das
 +
|Client-side library for Distributed Genome Annotation System
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|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Das/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Das]]
 +
|-
 +
|p5-Bio-Das-Lite
 +
|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]]
 +
|-
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|p5-Bio-FeatureIO
 +
|Handler for FeatureIO
 +
|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-FeatureIO/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-FeatureIO]]
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|-
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|p5-Bio-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]]
 +
|-
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|p5-Bio-Glite
 +
|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]]
 +
|-
 +
|p5-Bio-Graphics
 +
|Generate GD Images of Bio::Seq Objects
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|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Graphics/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Graphics]]
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|-
 +
|p5-Bio-MAGETAB
 +
|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]]
 +
|-
 +
|p5-Bio-NEXUS
 +
|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]]
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|-
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|p5-Bio-Phylo
 +
|Phylogenetic analysis using Perl
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|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-Phylo/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-Phylo]]
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|-
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|p5-Bio-SCF
 +
|Read and Update SCF Chromatographic Sequence Files
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|[[https://svnweb.freebsd.org/ports/head/biology/p5-Bio-SCF/pkg-descr?revision=HEAD]] [[https://metacpan.org/release/Bio-SCF]]
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|-
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|p5-Bio-Variation
 +
|BioPerl variation-related functionality
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|[[https://metacpan.org/release/Bio-Variation]]
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|-
 +
|p5-BioPerl
 +
|Collection of Perl modules for bioinformatics
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|[[https://svnweb.freebsd.org/ports/head/biology/p5-BioPerl/pkg-descr?revision=HEAD]] [[https://bioperl.org/]]
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|-
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|p5-BioPerl-Run
 +
|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]]
 
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Revision as of 05:03, 15 January 2020

Welcome to theIcon Disti GhostBSD.png Biology
App/Package Abstract Addition or Link
CheckM Quality assessment tool for the microbial genomes [[1]] [[2]]
GroopM Metagenomic binning suite [[3]] [[4]]
InsightToolkit Insight Toolkit [[5]] [[6]]
Jellyfish Fast, memory-efficient counting of k-mers in DNA [[7]] [[8]]
abyss Assembly By Short Sequences: parallel, paired-end sequence assembler [[9]] [[10]]
afni Advanced Functional Neuro Imaging [[11]] [[12]]
artemis DNA sequence viewer and annotation tool [[13]] [[14]]
avida Auto-adaptive genetic system designed for ALife research [[15]] [[16]]
babel Converts among various molecular file formats [[17]] [[18]]
bamtools API and toolkit for handling BAM files [[19]]
biococoa Bioinformatics framework [[20]] [[21]]
canu Single molecule sequence assembler [[22]] [[23]]
cycle Calendar program for women [[24]] [[25]]
cytoscape Software to visualize molecular interaction networks, gene expression [[26]] [[27]]
dDocent Bash pipeline for RAD sequencing [[28]] [[29]]
emboss Collection of open source tools for genetic sequence analysis [[30]] [[31]]
figtree Graphical viewer of phylogenetic trees [[32]] [[33]]
garlic Molecular viewer, editor, and visualization program [[34]] [[35]]
gperiodic Displays a periodic table of the elements [[36]] [[37]]
haplohseq Identify regions of allelic imbalance [[38]] [[39]]
hhsuite Remote protein homology detection suite [[40]] [[41]]
igv Visualization tool for genomic datasets [[42]] [[43]]
jalview Viewer and editor for multiple sequence alignments [[44]] [[45]]
kallisto Quantify abundances of transcripts from RNA-Seq data [[46]] [[47]]
mafft Multiple alignment program for amino acid or nucleotide sequences [[48]] [[49]]
minc2 Medical Imaging NetCDF [[50]] [[51]]
molden Display molecular orbitals and electron densities in 2D and 3D [[52]] [[53]]
ncbi-blast NCBI implementation of Basic Local Alignment Search Tool [[54]] [[55]]
ncbi-cxx-toolkit- NCBI C++ Toolkit [[56]] [[57]]
p5-Bio-ASN1-EntrezGene Regular expression-based Perl Parser for NCBI Entrez Gene [[58]] [[59]]
p5-Bio-Cluster BioPerl cluster modules [[60]] [[61]]
p5-Bio-Coordinate Modules for working with biological coordinates ttps://svnweb.freebsd.org/ports/head/biology/p5-Bio-Coordinate/pkg-descr?revision=HEAD [[62]]
p5-Bio-DB-EMBL Database object interface for EMBL entry retrieval [[63]] [[64]]
p5-Bio-DB-NCBIHelper Collection of routines useful for queries to NCBI databases [[65]] [[66]]
p5-Bio-Das Client-side library for Distributed Genome Annotation System [[67]] [[68]]
p5-Bio-Das-Lite Perl extension for the DAS (HTTP+XML) Protocol [[69]] [[70]]
p5-Bio-FeatureIO Handler for FeatureIO [[71]] [[72]]
p5-Bio-GFF3 Fast low-level functions for parsing and formatting GFF3 [[73]] [[74]]
p5-Bio-Glite Perl Interface to G-language [[75]] [[76]]
p5-Bio-Graphics Generate GD Images of Bio::Seq Objects [[77]] [[78]]
p5-Bio-MAGETAB Data model and utility API for the MAGE-TAB format [[79]] [[80]]
p5-Bio-NEXUS Object-oriented Perl API for the NEXUS file format [[81]] [[82]]
p5-Bio-Phylo Phylogenetic analysis using Perl [[83]] [[84]]
p5-Bio-SCF Read and Update SCF Chromatographic Sequence Files [[85]] [[86]]
p5-Bio-Variation BioPerl variation-related functionality [[87]]
p5-BioPerl Collection of Perl modules for bioinformatics [[88]] [[89]]
p5-BioPerl-Run Wrapper modules for common bioinformatics tools [[90]] [[91]]
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