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

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

Species tree estimation from multi-copy gene trees

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

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

Species tree estimation from gene trees via quartets

Species tree estimation from gene trees via weighted 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