Difference between revisions of "Biology"

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|[[https://svnweb.freebsd.org/ports/head/biology/p5-BioPerl-Run/pkg-descr?revision=HEAD]] [[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]]
 
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|p5-TrimGalore
|[[]] [[]]
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|Wrapper around Cutadapt and FastQC for adapter and quality trimming
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|[[https://svnweb.freebsd.org/ports/head/biology/p5-TrimGalore/pkg-descr?revision=HEAD]] [[https://github.com/FelixKrueger/TrimGalore]]
 
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|pbcopper
|[[]] [[]]
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|Core C++ library for Pacific Biosciences tools
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|[[https://svnweb.freebsd.org/ports/head/biology/pbcopper/pkg-descr?revision=HEAD]] [[https://github.com/PacificBiosciences/pbcopper]]
 
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|prodigal
|[[]] [[]]
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|Protein-coding gene prediction for prokaryotic genomes
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|[[https://svnweb.freebsd.org/ports/head/biology/prodigal/pkg-descr?revision=HEAD]] [[https://github.com/hyattpd/Prodigal]]
 
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|py27-multiqc
|[[]] [[]]
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|Aggregate bioinformatics analysis reports across samples and tools
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|[[https://svnweb.freebsd.org/ports/head/biology/py-multiqc/pkg-descr?revision=HEAD]] [[https://pypi.python.org/pypi/multiqc]]
 
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|py27-pymol
|[[]] [[]]
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|OpenGL-based molecular visualization system
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|[[https://svnweb.freebsd.org/ports/head/science/py-pymol/pkg-descr?revision=HEAD]] [[https://pymol.org/2/]]
 
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|py37-chainer-chemistry
|[[]] [[]]
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|Library for deep learning in biology and chemistry
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|[[https://svnweb.freebsd.org/ports/head/science/py-chainer-chemistry/pkg-descr?revision=HEAD]] [[https://github.com/pfnet-research/chainer-chemistry]]
 
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Revision as of 06:12, 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]]
p5-TrimGalore Wrapper around Cutadapt and FastQC for adapter and quality trimming [[92]] [[93]]
pbcopper Core C++ library for Pacific Biosciences tools [[94]] [[95]]
prodigal Protein-coding gene prediction for prokaryotic genomes [[96]] [[97]]
py27-multiqc Aggregate bioinformatics analysis reports across samples and tools [[98]] [[99]]
py27-pymol OpenGL-based molecular visualization system [[100]] [[101]]
py37-chainer-chemistry Library for deep learning in biology and chemistry [[102]] [[103]]
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