biology - The NetBSD Packages Collection

Software for the biological sciences

There are 72 packages in this category:

R-popbio-2.7
Construction and Analysis of Matrix Population Models
ad2vcf-0.1.3
Add allelic depth info from a SAM stream to a VCF file
arka-0.11nb2
Graphic interface for the programs from the GP package
azara-2.7nb8
Programs to process and view NMR data
bcftools-1.12nb1
Tools for manipulating BCF and VCF variant call files
beagle-5.2
Phasing genotypes and imputing ungenotyped markers
bedtools-2.30.0
Swiss army knife for genome arithmetic
biolibc-0.1.3.2
Low-level high-performance bioinformatics library
bioperl-1.7.7nb2
Perl tools for computational molecular biology
bodr-9nb14
Blue Obelisk Data Repository
bowtie2-2.4.2nb1
Ultrafast, memory-efficient short read aligner
bwa-0.7.17nb5
Map low-divergent sequences against a large reference genome
canu-1.8nb10
Single molecule sequence assembler for genomes large and small
cdhit-4.6.4nb5
Clustering and comparing protein or nucleotide sequences
chemical-mime-data-0.1.94
Chemical mime and file type support for desktops
chemtool-1.6.14nb15
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
coordgenlibs-1.4.2nb2
2D coordinate generation for molecules
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
fastqc-0.11.9nb1
Quality control tool for high throughput sequence data
filter-fastq-0.0.0.20210527
Filter reads from a FASTQ file
fluctuate-1.4
Estimation of population growth rate
gabedit-2.4.8nb11
Graphical User Interface to computational chemistry packages
generand-0.1.2
Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
genesplicer-20030403
Computational Method for Splice Site Prediction
glimmer-2.13nb1
System for finding genes in microbial DNA
gnome-chemistry-utils-0.14.16nb6
GChemPaint, a 2D chemical editor and other programs
gp-0.26
Manipulate DNA/RNA sequence in a Unix fashion
gromacs-4.5.5nb14
Molecular dynamics package
hisat2-2.1.0.23nb5
Alignment program for mapping next-generation sequencing reads
hmmer-3.0
Implementation of profile HMM software for protein sequence analysis
htslib-1.12nb2
C library for high-throughput sequencing data formats
igv-2.9.2
Visualization tool for genomic datasets
kallisto-0.46.1
Quantify abundances of transcripts from RNA-Seq data
lucy-1.20
Sequence Cleanup Program
maeparser-1.2.4nb2
Parser for Maestro file format
miniasm-0.3
OLC-based de novo assembler for long reads
minimap2-2.18nb1
Sequence alignment program for noisy, long reads
molsketch-0.7.2nb1
Program for drawing molecular structures
mopac-7.0nb1
Molecular energy calculation program
mpqc-2.3.1nb11
The Massively Parallel Quantum Chemistry Program
mummer-3.20nb9
System for aligning whole genome sequences
ncbi-blast+-2.11.0
NCBI implementation of Basic Local Alignment Search Tool
nut-15.8
Record what you eat and analyze your meals
openbabel-3.1.1nb7
Chemistry file translation program
p5-Bio-ASN1-EntrezGene-1.73nb1
Regular expression-based Perl Parser for NCBI Entrez Gene
pdbalign-20030812
Prediction of Protein Secondary Structure and Active Sites
peak-classifier-0.1.1
Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
phylip-3.69
Phylogeny Inference Package
plink-1.07nb1
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
py38-biopython-1.74nb1
Python libraries for computational molecular biology
py38-cutadapt-3.4
Find and remove adapter sequences, primers, poly-A tails, etc
py38-dnaio-0.5.1
Read and write FASTQ and FASTA files
py27-mol-1.5.0.1nb8
Molecular Visualization System
py38-pydicom-1.3.0
Pure python package for working with DICOM files
racon-1.4.3
Genomic consensus builder
rasmol-2.7.3nb2
Molecular Graphics Visualisation Tool
samtools-1.12nb1
Tools for manipulating sequence alignment maps
sewer-2.6nb2
SEquence Analysis using WEb Resources
stacks-2.2nb5
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
vcf-split-0.1.2
Split a multi-sample VCF into single-sample VCFs
vcf2hap-0.1.3
Generate .hap file from VCF for haplohseq
vsearch-2.13.4
Versatile open-source tool for metagenomics
xylem-1.8.7
Tools for manipulation of genetic databases