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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