Phylogenetic orthology inference for comparative genomics
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Updated
Jun 1, 2024 - Python
Phylogenetic orthology inference for comparative genomics
Species tree estimation from gene trees via weighted quartets
Coalescent-Aware Species Tree Length Estimation in Substitution-units
Species tree estimation from gene trees via quartets
Rooting species trees under the multi-species coalescent model
Species tree estimation from multi-copy gene trees
Shell script pipeline for inferring ML gene trees for many loci (e.g. genomic RAD loci)
Dynamic Programming (DP) based software Software to Estimate Species Tree by maximizing triplet agreement.
TreeBeST: Tree Building guided by Species Tree (Ensembl Compara modifications)
A tool for divide-and-conquer tree estimation via a shared distance matrix
Genetic Algorithm for gene Tree Construction/Correction optimal under sequence likelihood and reconciliation score
Implementation of the Super-Reconciliation model for reconciling a set of trees accounting for segmental duplications and losses.
Compresses SimPhy datasets into a single gzipped file for all the gene trees and gzipped mulitple sequence alignments for all the loci.
NGSphy: phylogenomic simulation of next-generation sequencing data
AST: An Automated Sequence-Sampling Method for Improving the Taxonomic Diversity of Gene Phylogenetic Trees
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