Biology

Welcome to the 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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If you don't find a package, you are looking for, we recommend to search the Ports Collection.
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