Biology

Welcome to the Biology

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