Contact us Category listing - biology
((V)irtual = Package is only listed here)
R-popbio Construction and Analysis of Matrix Population Models
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
bioperl Perl tools for computational molecular biology
bioruby (V) Intergrated environment for Bioinformatics using Ruby
bkchem (V) Python based chemical structures editor
bodr Blue Obelisk Data Repository
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
fastDNAml Program derived from Joseph Felsenstein's version 3.3 DNAML
fastp Ultra-fast all-in-one FASTQ preprocessor
fluctuate Estimation of population growth rate
gabedit Graphical User Interface to computational chemistry packages
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
kallisto Quantify abundances of transcripts from RNA-Seq data
lucy Sequence Cleanup Program
mmdb (V) Macromolecular coordinate library
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
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-ase (V) Atomic Simulation Environment
py-biofrills (V) Bioinformatics utilities for molecular sequence analysis
py-biopython Python libraries for computational molecular biology
py-biskit (V) Python platform for structural bioinformatics
py-cclib (V) Parsers and algorithms for computational chemistry
py-chempy (V) Python package useful for solving problems in chemistry
py-cobrapy (V) Package for constraints-based modeling of biological networks
py-cogent (V) Cogent A toolkit for statistical analysis of biological sequences
py-csb (V) Computational Structural Biology Toolbox
py-deap (V) Distributed Evolutionary Algorithms in Python
py-epigrass (V) Epidemiological Geo-Referenced Analysis and Simulation System
py-geppy (V) Package for gene expression programming in Python
py-gnm (V) Python Gaussian Network Model
py-gpaw (V) Grid-based real-space PAW method DFT code
py-htseq (V) Framework to analyze data from high-throughput sequencing assays
py-mdtraj (V) The analysis of molecular dynamics trajectories
py-mmLib (V) Python Macromolecular Library
py-mol Molecular Visualization System
py-neo (V) Python package for representing electrophysiology data
py-nibabel (V) Access a multitude of neuroimaging data formats
py-nilearn (V) Statistical learning for neuroimaging in Python
py-prody (V) Python Package for Protein Dynamics Analysis
py-psychopy (V) Psychology and neuroscience software in python
py-pydicom Pure python package for working with DICOM files
py-pygr (V) Pygr graph database for bioinformatics
py-pyquante (V) Quantum chemistry in Python
py-pysam (V) Python module for reading, manipulating and writing genomic data sets
py-pysb (V) Python Systems Biology modeling framework
py-pyvib2 (V) Analyzing vibrational motion and vibrational spectra
py-spglib (V) Python bindings for finding and handling crystal symmetries
py-sumatra (V) Tracking projects based on numerical simulation or analysis
py-thermopy (V) Some utilities for Thermodynamics and Thermochemistry
py-varify (V) Clinical DNA Sequencing Analysis and Data Discovery
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
vsearch Versatile open-source tool for metagenomics
xylem Tools for manipulation of genetic databases