biology - The NetBSD Packages Collection

Software for the biological sciences

There are 81 packages in this category:

R-popbio-2.7
Construction and Analysis of Matrix Population Models
ad2vcf-0.1.6
Add allelic depth info from a SAM stream to a VCF file
arka-0.11nb2
Graphic interface for the programs from the GP package
atac-seq-1.1
Core tools needed for ATAC-Seq analysis
azara-2.7nb10
Programs to process and view NMR data
balance-tui-0.1.1
Balance chemical equations from the CLI
bcftools-1.17
Tools for manipulating BCF and VCF variant call files
beagle-5.2
Phasing genotypes and imputing ungenotyped markers
bedtools-2.30.0nb1
Swiss army knife for genome arithmetic
biolibc-0.2.4
Low-level high-performance bioinformatics library
biolibc-tools-0.1.4.1
High-performance bioinformatics tools based on biolibc
bioperl-1.7.7nb3
Perl tools for computational molecular biology
bodr-9nb18
Blue Obelisk Data Repository
bowtie2-2.4.4nb2
Ultrafast, memory-efficient short read aligner
bwa-0.7.17nb6
Map low-divergent sequences against a large reference genome
canu-1.8nb14
Single molecule sequence assembler for genomes large and small
cdhit-4.8.1nb1
Clustering and comparing protein or nucleotide sequences
chemical-mime-data-0.1.94
Chemical mime and file type support for desktops
chemtool-1.6.14nb18
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-1.4.2nb5
2D coordinate generation for molecules
fasda-0.1.2
Fast and simple differential analysis
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
fastq-trim-0.1.2
Lightening fast sequence read trimmer
fastqc-0.11.9nb2
Quality control tool for high throughput sequence data
fastx-toolkit-0.0.14.6nb1
CLI tools for Short-Reads FASTA/FASTQ files preprocessing
filter-fastq-0.0.0.20210527nb1
Filter reads from a FASTQ file
fluctuate-1.4
Estimation of population growth rate
gabedit-2.4.8nb14
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
gffread-0.12.7
GFF/GTF format conversions, filtering, FASTA extraction, etc
glimmer-2.13nb1
System for finding genes in microbial DNA
gnome-chemistry-utils-0.14.16nb13
GChemPaint, a 2D chemical editor and other programs
gp-0.26
Manipulate DNA/RNA sequence in a Unix fashion
gromacs-4.5.5nb18
Molecular dynamics package
hisat2-2.2.1nb2
Alignment program for mapping next-generation sequencing reads
hmmer-3.0
Implementation of profile HMM software for protein sequence analysis
htslib-1.17
C library for high-throughput sequencing data formats
igv-2.9.2
Visualization tool for genomic datasets
kallisto-0.48.0
Quantify abundances of transcripts from RNA-Seq data
lucy-1.20
Sequence Cleanup Program
maeparser-1.2.4nb5
Parser for Maestro file format
miniasm-0.3
OLC-based de novo assembler for long reads
minimap2-2.24
Sequence alignment program for noisy, long reads
molsketch-0.7.3nb2
Program for drawing molecular structures
mopac-7.0nb1
Molecular energy calculation program
mpqc-2.3.1nb12
The Massively Parallel Quantum Chemistry Program
mummer-3.20nb10
System for aligning whole genome sequences
ncbi-blast+-2.13.0nb5
NCBI implementation of Basic Local Alignment Search Tool
nut-15.8
Record what you eat and analyze your meals
openbabel-3.1.1nb15
Chemistry file translation program
p5-Bio-ASN1-EntrezGene-1.73nb2
Regular expression-based Perl Parser for NCBI Entrez Gene
pdbalign-20030812
Prediction of Protein Secondary Structure and Active Sites
peak-classifier-0.1.4.5
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-0.08nb6
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
py310-biopython-1.79
Python libraries for computational molecular biology
py310-cutadapt-3.5
Find and remove adapter sequences, primers, poly-A tails, etc
py310-dnaio-0.9.1
Read and write FASTQ and FASTA files
py310-macs2-2.2.7.1
Algorithm for identifying transcription factor binding sites
py310-pydicom-2.3.1
Pure python package for working with DICOM files
racon-1.4.3
Genomic consensus builder
rasmol-2.7.3nb2
Molecular Graphics Visualisation Tool
rna-seq-1.1
Core tools needed for RNA-Seq analysis
samtools-1.17
Tools for manipulating sequence alignment maps
sewer-2.6nb2
SEquence Analysis using WEb Resources
stacks-2.60nb2
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-0.1.5.4
Split a multi-sample VCF into single-sample VCFs
vcf2hap-0.1.6
Generate .hap file from VCF for haplohseq
vsearch-2.18.0
Versatile open-source tool for metagenomics
xmakemol-5.16h
Program for visualizing atomic and molecular systems
xylem-1.8.7
Tools for manipulation of genetic databases