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 |