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The NetBSD Packages Collection: biology

You are now in the directory "biology".

Software for the biological sciences

Here are the one-line descriptions for each of the 51 items in this directory:


arka-0.11nb2: Graphic interface for the programs from the GP package
azara-2.7nb7: Programs to process and view NMR data
bcftools-1.9nb2: Calling and manipulating files VCF and BCF formats
bioperl-1.007002nb2: Perl tools for computational molecular biology
bodr-9nb9: Blue Obelisk Data Repository
bwa-0.7.17nb3: Map low-divergent sequences against a large reference genome
canu-1.8nb3: Single molecule sequence assembler for genomes large and small
cdhit-4.6.4nb3: Clustering and comparing protein or nucleotide sequences
chemical-mime-data-0.1.94: Chemical mime and file type support for desktops
chemtool-1.6.14nb11: Program for drawing organic molecules
clustalw-2.1: General purpose multiple alignment program for DNA or proteins
coalesce-1.5.0.2nb1: Estimates effective population size and mutation rate
fastDNAml-1.2.2: Program derived from Joseph Felsenstein's version 3.3 DNAML
fastp-0.20.0: Ultra-fast all-in-one FASTQ preprocessor
fluctuate-1.4: Estimation of population growth rate
gabedit-2.4.8nb8: Graphical User Interface to computational chemistry packages
genesplicer-20030403: Computational Method for Splice Site Prediction
glimmer-2.13nb1: System for finding genes in microbial DNA
gnome-chemistry-utils-0.12.13nb29: GChemPaint, a 2D chemical editor and other programs
gp-0.26: Manipulate DNA/RNA sequence in a Unix fashion
gromacs-4.5.5nb8: Molecular dynamics package
hisat2-2.1.0.23nb2: Alignment program for mapping next-generation sequencing reads
hmmer-3.0: Implementation of profile HMM software for protein sequence analysis
htslib-1.9nb5: C library for high-throughput sequencing data formats
kallisto-0.45.0nb1: Quantify abundances of transcripts from RNA-Seq data
lucy-1.20: Sequence Cleanup Program
mopac-7.0nb1: Molecular energy calculation program
mpqc-2.3.1nb8: The Massively Parallel Quantum Chemistry Program
mummer-3.20nb7: System for aligning whole genome sequences
ncbi-blast+-2.8.1nb5: NCBI implementation of Basic Local Alignment Search Tool
nut-15.8: Record what you eat and analyze your meals
openbabel-2.3.2nb9: Chemistry file translation program
p5-Bio-ASN1-EntrezGene-1.72nb2: Regular expression-based Perl Parser for NCBI Entrez Gene
pdbalign-20030812: Prediction of Protein Secondary Structure and Active Sites
phylip-3.69: Phylogeny Inference Package
plink-1.07: Whole-genome association analysis toolset
plinkseq-0.08nb3: C/C++ library for working with human genetic variation data
primer3-2.3.6: Design PCR primers
profit-2.2nb1: Performs least squares fits of two protein structures
puzzle-5.2: Maximum likelihood analysis of molecular sequence data
py37-biopython-1.74: Python libraries for computational molecular biology
py27-mol-1.5.0.1nb6: Molecular Visualization System
py37-pydicom-1.2.1: Pure python package for working with DICOM files
rasmol-2.7.3nb2: Molecular Graphics Visualisation Tool
samtools-1.9nb2: Tools for manipulating next-generation sequencing data
sewer-2.6nb2: SEquence Analysis using WEb Resources
stacks-2.2nb2: Software pipeline for building loci from short-read sequences
stride-20030804: Protein secondary structure assignment from atomic coordinates
Trimmomatic-0.38: Flexible read trimming tool for Illumina NGS data
vsearch-2.13.4: Versatile open-source tool for metagenomics
xylem-1.8.7: Tools for manipulation of genetic databases


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