Contact us Category listing - biology
((V)irtual = Package is only listed here)
ad2vcf Add allelic depth info from a SAM stream to a VCF file
arka Graphic interface for the programs from the GP package
azara Programs to process and view NMR data
bcftools Tools for manipulating BCF and VCF variant call files
beagle Phasing genotypes and imputing ungenotyped markers
bedtools Swiss army knife for genome arithmetic
biolibc Low-level high-performance bioinformatics library
bioperl Perl tools for computational molecular biology
bodr Blue Obelisk Data Repository
bowtie2 Ultrafast, memory-efficient short read aligner
bwa Map low-divergent sequences against a large reference genome
canu Single molecule sequence assembler for genomes large and small
cdhit Clustering and comparing protein or nucleotide sequences
chemical-mime-data Chemical mime and file type support for desktops
chemtool Program for drawing organic molecules
clustalw General purpose multiple alignment program for DNA or proteins
coalesce Estimates effective population size and mutation rate
coordgenlibs 2D coordinate generation for molecules
fastDNAml Program derived from Joseph Felsenstein's version 3.3 DNAML
fastp Ultra-fast all-in-one FASTQ preprocessor
fastqc Quality control tool for high throughput sequence data
filter-fastq Filter reads from a FASTQ file
fluctuate Estimation of population growth rate
gabedit Graphical User Interface to computational chemistry packages
generand Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
genesplicer Computational Method for Splice Site Prediction
glimmer System for finding genes in microbial DNA
gnome-chemistry-utils GChemPaint, a 2D chemical editor and other programs
gp Manipulate DNA/RNA sequence in a Unix fashion
gromacs Molecular dynamics package
hisat2 Alignment program for mapping next-generation sequencing reads
hmmer Implementation of profile HMM software for protein sequence analysis
htslib C library for high-throughput sequencing data formats
igv Visualization tool for genomic datasets
kallisto Quantify abundances of transcripts from RNA-Seq data
lucy Sequence Cleanup Program
maeparser Parser for Maestro file format
miniasm OLC-based de novo assembler for long reads
minimap2 Sequence alignment program for noisy, long reads
molsketch Program for drawing molecular structures
mopac Molecular energy calculation program
mpqc The Massively Parallel Quantum Chemistry Program
mummer System for aligning whole genome sequences
ncbi-blast+ NCBI implementation of Basic Local Alignment Search Tool
nut Record what you eat and analyze your meals
openbabel Chemistry file translation program
p5-Bio-ASN1-EntrezGene Regular expression-based Perl Parser for NCBI Entrez Gene
pdbalign Prediction of Protein Secondary Structure and Active Sites
peak-classifier Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
phylip Phylogeny Inference Package
plink Whole-genome association analysis toolset
plinkseq C/C++ library for working with human genetic variation data
primer3 Design PCR primers
profit Performs least squares fits of two protein structures
puzzle Maximum likelihood analysis of molecular sequence data
py-biopython Python libraries for computational molecular biology
py-cutadapt Find and remove adapter sequences, primers, poly-A tails, etc
py-dnaio Read and write FASTQ and FASTA files
py-mol Molecular Visualization System
py-pydicom Pure python package for working with DICOM files
R-popbio Construction and Analysis of Matrix Population Models
racon Genomic consensus builder
rasmol Molecular Graphics Visualisation Tool
samtools Tools for manipulating sequence alignment maps
sewer SEquence Analysis using WEb Resources
stacks Software pipeline for building loci from short-read sequences
stride Protein secondary structure assignment from atomic coordinates
trimmomatic Flexible read trimming tool for Illumina NGS data
vcf-split Split a multi-sample VCF into single-sample VCFs
vcf2hap Generate .hap file from VCF for haplohseq
vsearch Versatile open-source tool for metagenomics
xylem Tools for manipulation of genetic databases