biology - The NetBSD Packages Collection

Software for the biological sciences

There are 90 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-1.4
Core tools needed for ATAC-Seq analysis
azara-2.7nb10
Programs to process and view NMR data
balance-tui-0.1.2
Balance chemical equations from the CLI
bcftools-1.17nb1
Tools for manipulating BCF and VCF variant call files
beagle-5.2
Phasing genotypes and imputing ungenotyped markers
bedtools-2.31.1
Swiss army knife for genome arithmetic
biolibc-0.2.6
Low-level high-performance bioinformatics library
biolibc-tools-0.1.4.13
High-performance bioinformatics tools based on biolibc
bioperl-1.7.7nb4
Perl tools for computational molecular biology
bodr-9nb20
Blue Obelisk Data Repository
bowtie2-2.5.3
Ultrafast, memory-efficient short read aligner
bwa-0.7.17nb7
Map low-divergent sequences against a large reference genome
canu-2.2nb2
Single molecule sequence assembler for genomes large and small
cdhit-4.8.1nb1
Clustering and comparing protein or nucleotide sequences
chemtool-1.6.14nb21
Program for drawing organic molecules
chip-seq-1.2
Core tools needed for ChIP-Seq analysis
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-1.4.2nb7
2D coordinate generation for molecules
fasda-0.1.5
Fast and simple differential analysis
fastDNAml-1.2.2
Program derived from Joseph Felsenstein's version 3.3 DNAML
fastp-0.22.0
Ultra-fast all-in-one FASTQ preprocessor
fastq-trim-0.1.3
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-0.0.0.20210527nb2
Filter reads from a FASTQ file
fluctuate-1.4
Estimation of population growth rate
gabedit-2.4.8nb17
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
gp-0.26
Manipulate DNA/RNA sequence in a Unix fashion
gromacs-4.5.5nb20
Molecular dynamics package
hisat2-2.2.1nb4
Alignment program for mapping next-generation sequencing reads
hmmer-3.0
Implementation of profile HMM software for protein sequence analysis
htslib-1.17nb3
C library for high-throughput sequencing data formats
igv-2.9.2
Visualization tool for genomic datasets
kallisto-0.50.1
Quantify abundances of transcripts from RNA-Seq data
libpll-0.3.2nb1
High-performance software library for phylogenetic analysis
lucy-1.20
Sequence Cleanup Program
maeparser-1.2.4nb7
Parser for Maestro file format
microsynteny-tools-0.1.0.175
Tools for exploring microsyntenic differences among species
miniasm-0.3
OLC-based de novo assembler for long reads
minimap2-2.24nb1
Sequence alignment program for noisy, long reads
molsketch-0.8.0nb6
Program for drawing molecular structures
mopac-22.0.6nb1
Semi-empirical (MNDO, etc.) molecular orbital calculation
mpqc-2.3.1nb12
The Massively Parallel Quantum Chemistry Program
mummer-3.20nb10
System for aligning whole genome sequences
ncbi-blast+-2.14.1nb2
NCBI implementation of Basic Local Alignment Search Tool
nut-15.8
Record what you eat and analyze your meals
openbabel-3.1.1nb23
Chemistry file translation program
p5-Bio-ASN1-EntrezGene-1.73nb3
Regular expression-based Perl Parser for NCBI Entrez Gene
pdbalign-20030812
Prediction of Protein Secondary Structure and Active Sites
peak-classifier-0.1.4.13
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-0.08nb9
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
py311-bcbio-gff-0.7.0
Read and write Generic Feature Format (GFF) with Biopython integration
py311-biopython-1.81
Python libraries for computational molecular biology
py311-cutadapt-4.6
Find and remove adapter sequences, primers, poly-A tails, etc
py311-dna-features-viewer-3.1.3
Python library to visualize DNA features, e.g. GenBank or Gff files
py311-dnaio-1.2.0
Read and write FASTQ and FASTA files
py311-macs2-2.2.9.1
Algorithm for identifying transcription factor binding sites
py311-macs3-3.0.0
Peak caller aimed at transcription factor binding sites
py311-multiqc-1.14
Aggregate bioinformatics analysis reports across samples and tools
py311-pydicom-2.4.4
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-1.2.2nb1
Core tools needed for RNA-Seq analysis
rna-star-2.7.10b
Spliced Transcripts Alignment to a Reference
samtools-1.17nb1
Tools for manipulating sequence alignment maps
seqtk-1.4
Tool for processing sequences in FASTA/FASTQ format
sewer-2.6nb2
SEquence Analysis using WEb Resources
sra-tools-3.0.6nb2
NCBI's toolkit for handling data in INSDC Sequence Read Archives
stacks-2.60nb3
Software pipeline for building loci from short-read sequences
stride-20030804
Protein secondary structure assignment from atomic coordinates
stringtie-2.1.1
Transcript assembly and quantification for RNA-seq
Trimmomatic-0.38
Flexible read trimming tool for Illumina NGS data
vcf-split-0.1.5.10
Split a multi-sample VCF into single-sample VCFs
vcf2hap-0.1.6.7
Generate .hap file from VCF for haplohseq
vsearch-2.27.0
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