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dadi is a bioinformatics tool for inferring demographic history and selection from genetic data using diffusion approximations, offering speed and flexibility in modeling population dynamics. It supports up to three populations with customizable parameters and provides efficient computational performance.

Offline tool for cleaning tables of human gene and protein identifiers (TXT, CSV, TSV, XLSX). It maps approved symbols, aliases, previous symbols, Ensembl gene, UniProt, Entrez, RefSeq and HGNC identifiers to current HGNC approved symbols with cross-references, using a bundled HGNC snapshot. Excel date-corrupted symbols are recovered where the original is unambiguous and flagged for manual review otherwise; no input row is dropped. Each run records the tool version and HGNC release and writes a per-row audit table.

BacSelect is a reproducible resource for selecting compact, nested panels of complete bacterial genome assemblies that span genome architecture. From a defined and versioned public genome universe, BacSelect deterministically selects assemblies so users can choose a panel size from N=10–500 while retaining nestedness across scales. Versioned releases provide genome-panel manifests, downloadable assemblies, structural-coverage information, checksums and provenance for reproducible benchmarking, method development and comparative genomics.

RAiSD-AI is a tool for training, testing, and deploying Convolutional Neural Networks to detect selective sweeps in genomic data, extending the functionality of the original RAiSD software with machine learning capabilities. It supports SNP data processing, CNN model training with TensorFlow or PyTorch, and genome-wide selective sweep detection.

GAIn is a platform for annotating genetic variants, genomic positions, and regions with reproducible, declarative pipelines using curated Genomic Resource Repositories.

blue-crab is a tool to convert from ONT POD5 format to the community maintained SLOW5/BLOW5 format. Lossless nanopore pod5 s/blow5 file conversion.

Exact, validated excision of coordinate-defined genomic regions from transposed NEXUS matrices.

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

A Python script that converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate.

NuclearPhaser is a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs. This is an overview of the phasing pipeline for dikaryons.