species-tree

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

Easily construct the ML species tree with single-copy gene shared by different species.

wQFM implementation in Java

Bash scripts for analysis of Hyb-Seq data (from raw reads to species trees/networks)

Reproducible phylogenomics pipeline that builds partitioned species trees from BUSCO v5 results.

Set of scripts to process HybSeq target enrichment HTS data (on computing grids).

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

split-based gene tree–species tree reconciliation for robust branch mapping under missing taxa

Adaptive HGT-aware phylogenomic pipeline for prokaryotic marker gene selection and species tree inference — pip install markerfinder (PyPI)

Python 3 rewrite of MaxTiC: rank species-tree internal nodes by Maximum Time Consistency under lateral-gene-transfer constraints. Zero runtime dependencies, reproducible rankings, multi-format reconciliation adapters, robustness analysis, HTML reporting, Docker/Singularity/Nextflow/Snakemake. 📦 pip install MaxTiC-Next

A pipeline to reconstruct a species tree with RaxML, from Single-Copy Orthologues (SCOs) identified by OrthoFinder.

This is a Snakemake workflow that calculates maximum-likelihood gene trees with IQ-TREE and 100 bootstrap replicates for each tree. Then, consensus trees are produced and combined to infer a species tree following the multispecies coalescent model with ASTRAL. Imported from my GitLab.

A highly scalable implementation of SimPhy for the simulation of species, locus and gene trees under gene duplication, loss, transfer and the multispecies coalescent. It supports multi-core parallelism and linear memory, and reproduces SimPhy 1.0.2 output exactly. Derived from SimPhy by Mallo, de Oliveira Martins and Posada (2016).