ASTER
Accurate Species Tree EstimatoR series; a family of optimation algorithms for species tree inference implemented in C++.
Availability
| Cluster | Module/Version |
|---|---|
| BOSE | aster/1.25 |
| BGSC | None |
Note: You can simply use module load aster to activate the most recently installed version of this software.
Commands
This is a list of each of the commands available within ASTER we wanted to highlight. Click the links below for a full list of the individual arguments and instructions.
| Command | Description | Online Manual |
|---|---|---|
| astral4 | Accurate Species Tree ALgorithm (ASTRAL-IV) | Online Manual |
| astral-pro3 | Accurate Species Tree ALgorithm for PaRalogs and Orthologs (ASTRAL-Pro3) | Online Manual |
| caster-site | Coalescence-aware Alignment-based Species Tree EstimatoR (CASTER) | Online Manual |
| wastral | Weighted ASTRAL (wASTRAL) | Online Manual |
| waster | Without-Alignment/Assembly Species Tree EstimatoR (WASTER) | Online Manual |
Multi-Threading
Several tools have built-in support for multi-threading, which can significantly increase performance of the tool you are wanting to use. Add -t $SLURM_NTASKS to your command to automatically use the number of CPU cores you requested for your Slurm job. View the advanced options for each tool within the documentation site for additional information.
Sample Slurm Script
#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]
# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32 # How many CPU cores do you want to request
#SBATCH --nodes=1 # How many nodes do you want to request
# -- SCRIPT COMMANDS -- #
# Load the needed modules
module load aster/1.25 # Load ASTER
astral-pro3 -t $SLURM_NTASKS myfile.nw
Citation
Please include the following citation in your papers to support continued development of ASTER. Each tool included with ASTER also has its own citation you should include in any papers, which can be found in the tutorial directory within the GitHub site for ASTER.
Chao Zhang, Rasmus Nielsen, Siavash Mirarab, ASTER: A Package for Large-scale Phylogenomic Reconstructions, Molecular Biology and Evolution, 2025, msaf172, https://doi.org/10.1093/molbev/msaf172