| Package Name | Access | Summary | Updated |
|---|---|---|---|
| dendropy | public | A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. | 2025-06-25 |
| beav | public | beav: Bacterial genome and mobile element annotation pipeline | 2025-06-25 |
| demultiplex | public | Demultiplex any number of FASTA or a FASTQ files based on a list of barcodes | 2025-06-25 |
| shortcut | public | ShortCut Small RNA-seq data trimmer and quality control tool | 2025-06-25 |
| lepwrap | public | The Snakemake pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring+orienting genome assemblies. | 2025-06-25 |
| mi-pimento | public | A PrIMEr infereNce TOolkit to facilitate large-scale calling of metabarcoding amplicon sequence variants. | 2025-06-25 |
| pybascule | public | Bayesian NMF signatures deconvolution and DP clustering. | 2025-06-25 |
| strainr2 | public | StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities using metagenomic sequencing reads | 2025-06-25 |
| ucsc-fasplit | public | Split an fa file into several files. | 2025-06-25 |
| ucsc-fasomerecords | public | Extract multiple fa records. | 2025-06-25 |
| ucsc-bigwigsummary | public | Extract summary information from a bigWig file. | 2025-06-25 |
| learnmsa | public | learnMSA: Learning and Aligning large Protein Families | 2025-06-25 |
| kneaddata | public | KneadData is a tool designed to perform quality control on metagenomic sequencing data. | 2025-06-25 |
| irida-uploader | public | Upload NGS data to IRIDA system. | 2025-06-25 |
| dampa | public | DAMPA designs probes for use in targetted metagenomics. It leverages pangenome graphs to increase speed and accuracy. | 2025-06-25 |
| biobb_godmd | public | Biobb_godmd is a BioBB category for GOdMD tool (protein conformational transitions). | 2025-06-25 |
| ssm | public | Secondary-structure matching, tool for fast protein structure alignment | 2025-06-25 |
| ucsc-fasize | public | Print total base count in fa files. | 2025-06-24 |
| clipper | public | Crystallographic automation and complex data manipulation libraries. | 2025-06-24 |
| dadaist2 | public | Command line wrapper to run DADA2 on a set of paired-end reads | 2025-06-24 |
| vbz-h5py-plugin | public | Oxford Nanopore Technologies VBZ HDF plugin for h5py. | 2025-06-24 |
| gafpack | public | Convert alignments to pangenome variation graphs to coverage maps | 2025-06-24 |
| blobtoolkit | public | Interactive quality assessment of genome assemblies. | 2025-06-24 |
| argnorm | public | Normalize antibiotic resistance genes (ARGs) abundance tables (e.g., from metagenomics) by using the ARO ontology (developed by CARD). | 2025-06-24 |
| tssv | public | Targeted characterisation of short structural variation. | 2025-06-24 |
