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
atac-seq Core tools needed for ATAC-Seq analysis
azara Programs to process and view NMR data
balance-tui Balance chemical equations from the CLI
bcf-score Bcftools plugin for mosaic chromosomal alteration analysis
bcftools Tools for manipulating BCF and VCF variant call files
beagle Phasing genotypes and imputing ungenotyped markers
bedtools Swiss army knife for genome arithmetic
bio-mocha Bcftools plugin for mosaic chromosomal alteration analysis
biolibc Low-level high-performance bioinformatics library
biolibc-tools High-performance bioinformatics tools based on biolibc
bioperl Perl tools for computational molecular biology
bioruby (V) Intergrated environment for Bioinformatics using Ruby
biostar-tools (V) Meta-package for Biostar Handbook tools
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
chemtool Program for drawing organic molecules
chip-seq Core tools needed for ChIP-Seq analysis
clustalw General purpose multiple alignment program for DNA or proteins
coalesce Estimates effective population size and mutation rate
coordgenlibs 2D coordinate generation for molecules
fasda Fast and simple differential analysis
fastDNAml Program derived from Joseph Felsenstein's version 3.3 DNAML
fastp Ultra-fast all-in-one FASTQ preprocessor
fastq-trim Lightening fast sequence read trimmer
fastqc Quality control tool for high throughput sequence data
fasttree Approximately-maximum-likelihood phylogenetic trees from alignments
fastx-toolkit CLI tools for Short-Reads FASTA/FASTQ files preprocessing
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
gffread GFF/GTF format conversions, filtering, FASTA extraction, etc
glimmer System for finding genes in microbial DNA
gp Manipulate DNA/RNA sequence in a Unix fashion
gromacs Molecular dynamics package
haplohseq Identify regions of allelic imbalance
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
jmol (V) Jmol: an open-source Java viewer for chemical structures in 3D
kallisto Quantify abundances of transcripts from RNA-Seq data
libpll High-performance software library for phylogenetic analysis
lucy Sequence Cleanup Program
maeparser Parser for Maestro file format
mca-calling Core tools for Mosaic Chromosomal Alteration event calling
microsynteny-tools Tools for exploring microsyntenic differences among species
miniasm OLC-based de novo assembler for long reads
minimap2 Sequence alignment program for noisy, long reads
mmdb (V) Macromolecular coordinate library
molsketch Program for drawing molecular structures
mopac Semi-empirical (MNDO, etc.) molecular orbital calculation
mpqc The Massively Parallel Quantum Chemistry Program
mummer System for aligning whole genome sequences
nanocomp (V) Compare runs of Oxford Nanopore sequencing data and alignments
nanofilt (V) Filtering and trimming of Oxford Nanopore sequencing data
nanoget (V) Extract information from Oxford Nanopore sequencing data
nanolyse (V) Removing reads mapping to the lambda genome
nanomath (V) Math functions for other Oxford Nanopore processing scripts
nanoplot (V) Plotting suite for Oxford Nanopore sequencing data and alignments
nanoQC (V) Create fastQC-like plots for Oxford Nanopore sequencing data
nanostat (V) Statistics for Oxford Nanopore sequencing data and alignments
ncbi-blast+ NCBI implementation of Basic Local Alignment Search Tool
nutsqlite 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-ase (V) Atomic Simulation Environment
py-bcbio-gff Read and write Generic Feature Format (GFF) with Biopython integration
py-biofrills (V) Bioinformatics utilities for molecular sequence analysis
py-biopython Python libraries for computational molecular biology
py-cantera (V) Chemical kinetics, thermodynamics, and transport tool suite
py-cclib (V) Parsers and algorithms for computational chemistry
py-chemicals (V) Chemical properties component of ChEDL library
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-cutadapt Find and remove adapter sequences, primers, poly-A tails, etc
py-deap (V) Distributed Evolutionary Algorithms in Python
py-dna-features-viewer Python library to visualize DNA features, e.g. GenBank or Gff files
py-dnaio Read and write FASTQ and FASTA files
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) Python library to facilitate programmatic analysis of sequence data
py-macs2 Algorithm for identifying transcription factor binding sites
py-macs3 Peak caller aimed at transcription factor binding sites
py-mappy (V) Minimap2 python binding
py-mdanalysis (V) Library to analyze and manipulate molecular dynamics trajectories
py-mdtraj (V) The analysis of molecular dynamics trajectories
py-mmLib (V) Python Macromolecular Library
py-multiqc Aggregate bioinformatics analysis reports across samples and tools
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-pydeseq2 (V) Python implementation of the popular DESeq2 R package
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-spglib (V) Python bindings for finding and handling crystal symmetries
py-sumatra (V) Tracking projects based on numerical simulation or analysis
py-thermo (V) Chemical properties component of ChEDL
py-thermopy (V) Some utilities for Thermodynamics and Thermochemistry
py-varify (V) Clinical DNA Sequencing Analysis and Data Discovery
R-popbio Construction and Analysis of Matrix Population Models
R-rgbif (V) Interface to the Global Biodiversity Information Facility API
racon Genomic consensus builder
rasmol Molecular Graphics Visualisation Tool
readseq (V) Read and reformat biosequences, Java command-line version
rna-seq Core tools needed for RNA-Seq analysis
rna-star Spliced Transcripts Alignment to a Reference
samtools Tools for manipulating sequence alignment maps
seqtk Tool for processing sequences in FASTA/FASTQ format
sewer SEquence Analysis using WEb Resources
sra-tools NCBI's toolkit for handling data in INSDC Sequence Read Archives
stacks Software pipeline for building loci from short-read sequences
stride Protein secondary structure assignment from atomic coordinates
stringtie Transcript assembly and quantification for RNA-seq
subread High-performance read alignment, quantification and mutation discovery
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
xmakemol Program for visualizing atomic and molecular systems
xylem Tools for manipulation of genetic databases