Gentrius: Identifying equally scoring trees in phylogenomics with incomplete data

by Olga Chernomor, Christiane Elgert, and Arndt von Haeseler 2023

This repository contains Data and Code used in the manuscript: bioRxiv: https://doi.org/10.1101/2023.01.19.524678

Gentrius - GENerating Trees from Incomplete Unrooted Subtrees

The Gentrius algorithm is implemented in IQ-TREE 2 (C++) and is available since version 2.2. The source code is available from https://github.com/iqtree/iqtree2.

1. System requirements

• All software dependencies and operating systems (including version numbers): IQ-TREE 2 is available for Windows/macOS/Linux (pre-compiled binaries are available from http://www.iqtree.org). All required libraries are distributed with IQ-TREE 2 code.
• Versions the software has been tested on: Gentrius was tested in IQ-TREE v.2.2
• Any required non-standard hardware: none

2. Installation guide

• Instructions: Extensive instructions are available at http://www.iqtree.org/doc/Quickstart
• Typical install time on a "normal" desktop computer: installation from the source code takes about 15 mins

3. Manual and Demo

• Instructions to run on data: for the manual specific to analysis with Gentrius see manual
• Demo dataset: available in example
• Expected run time for demo on a "normal" desktop computer: 38s

4. Instructions for use

• How to run the software on data from the manuscript: the script to run Gentrius on datasets without consensus tree is available in run Gentrius and to run analysis with consensus tree run consensus
• Reproduction instructions: the scripts used to analyse datasets from the manuscript are available at reproduce bio script

Matrix Simulator - Generating 0/1 matrices

https://github.com/OlgaChern/MatrixSimulator