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BEAST2 — Bayesian Evolutionary Analysis by Sampling Trees. Cross-platform Java application for Bayesian phylogenetic inference using MCMC sampling. Use when estimating time-calibrated phylogenies, rel

2 shared topics • 1 shared operation

Ensembl Database — EMBL-EBI's comprehensive genome annotation database covering 300+ species with gene models, variants, regulatory features, and comparative genomics. Query via REST API at rest.ensem

2 shared topics • 1 shared operation

LAST — adaptive-seed sequence aligner for genomes, long reads, and proteins. Uses lastdb to build databases, last-train to learn substitution/gap rates, lastal for alignment, last-split for rearrangem

2 shared topics • 1 shared operation

MAFFT — multiple sequence alignment for nucleotide and protein sequences. Implements progressive (FFT-NS-1, FFT-NS-2), iterative refinement (FFT-NS-i), and consistency-based iterative methods (L-INS-i

2 shared topics • 1 shared operation

OrthoFinder — fast, accurate ortholog inference for comparative genomics. Identifies orthogroups, orthologs, gene trees, rooted species trees, and gene duplication events from protein or nucleotide se

2 shared topics • 1 shared operation