| Package Name | Access | Summary | Updated |
|---|---|---|---|
| segemehl | public | Short read mapping with gaps | 2025-09-30 |
| rainbow | public | Efficient tool for clustering and assembling short reads, especially for RAD | 2025-09-30 |
| stacks | public | Stacks is a software pipeline for building loci from short-read sequences. | 2025-09-30 |
| genomepy | public | Install and use genomes & gene annotations the easy way! | 2025-09-30 |
| kraken | public | Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. | 2025-09-30 |
| snpeff | public | Genetic variant annotation and effect prediction toolbox | 2025-09-30 |
| rnacode | public | RNAcode - Analyze the protein coding potential in multiple sequence alignments RNAcode relies on evolutionary signatures including synonymous/conservative mutations and conservation of the reading frame. It does not use any species specific sequence characteristics whatsoever and does not use any machine learning techniques. | 2025-09-30 |
| sweepfinder2 | public | The BWA read mapper. | 2025-09-29 |
| r-structssi | public | Performs multiple testing corrections that take specific structure of hypotheses into account. | 2025-09-29 |
| pysradb | public | Python package for retrieving metadata and downloading datasets from SRA/ENA/GEO | 2025-09-29 |
| gatk4 | public | Genome Analysis Toolkit (GATK4) | 2025-09-29 |
| perl-extutils-parsexs | public | Converts Perl XS code into C code. | 2025-09-27 |
| spades | public | SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies. | 2025-09-27 |
| randfold | public | No Summary | 2025-09-26 |
| maxbin2 | public | MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. | 2025-09-26 |
| corset | public | Software for clustering de novo assembled transcripts and counting overlapping reads. | 2025-09-26 |
| ephemeris | public | Ephemeris is an opinionated library and set of scripts for managing the bootstrapping of Galaxy project plugins - tools, index data, and workflows. | 2025-09-26 |
| spaln | public | Map and align a set of cDNA/EST or protein sequences onto a genome. | 2025-09-26 |
| kma | public | KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. | 2025-09-26 |
| ensembl-vep | public | Ensembl Variant Effect Predictor | 2025-09-26 |
| clustalo | public | Latest version of Clustal: a multiple sequence alignment program for DNA or proteins | 2025-09-26 |
| emboss | public | The European Molecular Biology Open Software Suite | 2025-09-26 |
| consel | public | CONSEL calculates the probability value (i.e., p-value) to assess the confidence in the selection problem. Although CONSEL is applicable to any selection problem, it is mainly designed for the phylogenetic tree selection | 2025-09-26 |
| kmc | public | Tools for efficient k-mer counting and filtering of reads based on k-mer content. | 2025-09-25 |
| snakemake | public | A popular workflow management system aiming at full in-silico reproducibility. | 2025-09-25 |
