Phylogenetic orthology inference for comparative genomics

TreeBeST: Tree Building guided by Species Tree (Ensembl Compara modifications)

NGSphy: phylogenomic simulation of next-generation sequencing data

A tool for divide-and-conquer tree estimation via a shared distance matrix

Species tree estimation from multi-copy gene trees

Shell script pipeline for inferring ML gene trees for many loci (e.g. genomic RAD loci)

Genetic Algorithm for gene Tree Construction/Correction optimal under sequence likelihood and reconciliation score

Coalescent-Aware Species Tree Length Estimation in Substitution-units

Dynamic Programming (DP) based software Software to Estimate Species Tree by maximizing triplet agreement.

Implementation of the Super-Reconciliation model for reconciling a set of trees accounting for segmental duplications and losses.

Rooting species trees under the multi-species coalescent model

Species tree estimation from gene trees via weighted quartets

AST: An Automated Sequence-Sampling Method for Improving the Taxonomic Diversity of Gene Phylogenetic Trees

Species tree estimation from gene trees via quartets

Compresses SimPhy datasets into a single gzipped file for all the gene trees and gzipped mulitple sequence alignments for all the loci.

Datasets and scripts for "Coalescent-based branch length estimation improves dating of species trees" paper