A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

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

Clann: constructing consensus trees and supertrees from multiple source trees

NGSphy: phylogenomic simulation of next-generation sequencing data

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

Two pipelines to perform phylogenomic analysis

Species tree estimation from multi-copy gene trees

Parse taxonomic data from Catalog Of Life to a graph database.

Coalescent-Aware Species Tree Length Estimation in Substitution-units

Rooting species trees under the multi-species coalescent model

Species tree estimation from gene trees via quartets

Species tree estimation from gene trees via weighted quartets

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

Datasets and scripts for "Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss" paper

Datasets and scripts used in "Phylogenomic branch length estimation using quartets" paper

Datasets and scripts used in "Quintet Rooting: rooting species trees under the multi-species coalescent model" paper

Materials for course about processing HybSeq data on computing grids