OrthoFinder

ASTRAL — fast species tree estimation from unrooted gene trees under the multi-species coalescent model. Handles incomplete lineage sorting (ILS) in phylogenomic datasets with hundreds of species and

3 shared topics • 2 shared operations

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

3 shared topics • 2 shared operations

Ensembl Compara — comparative genomics database and API from EMBL-EBI providing pairwise and multiple whole-genome alignments, gene trees, protein families, orthologues, paralogues, and synteny region

3 shared topics • 2 shared operations

TreeTime — maximum likelihood molecular clock inference, ancestral sequence reconstruction, and phylodynamic analysis from time-stamped phylogenies. Infers timetrees by iteratively optimizing ancestra

3 shared topics • 2 shared operations

IQ-TREE ModelFinder routing skill for maximum-likelihood phylogenetic model selection, partition merging, and reproducible tree inference from aligned DNA, amino-acid, codon, binary, morphological, an

3 shared topics • 1 shared operation