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Accurate Species Tree ALgorithm for PaRalogs and Orthologs (ASTRAL-Pro3)

ASTRAL-Pro stands for ASTRAL for PaRalogs and Orthologs. ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees and is statistically consistent under the multi-species coalescent model (and thus is useful for handling incomplete lineage sorting, i.e., ILS). ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-pro finds the species tree that has the maximum number of shared induced quartet tree equivalent classes with the set of gene trees, subject to the constraint that the set of bipartitions in the species tree comes from a predefined set of bipartitions. Please see the paper below for the definition of the PL-quartet scores, which is what ASTRAL-Pro optimizes. We refer to the tool both as A-Pro and ASTRAL-Pro.

ASTRAL-Pro3 re-implements ASTRAL-Pro in an equally accurate yet faster, and easier to install and lower memory consumption way. ASTRAL-Pro3 also integrates CASTLES-Pro and thus computes terminal and internal branch lengths in substitution-per-site units.

Publication

[1] Chao Zhang, Siavash Mirarab, ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees, Bioinformatics, 2022, btac620, https://doi.org/10.1093/bioinformatics/btac620

[2] Chao Zhang, Celine Scornavacca, Erin K Molloy, Siavash Mirarab, ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy, Molecular Biology and Evolution, Volume 37, Issue 11, November 2020, Pages 3292–3307, https://doi.org/10.1093/molbev/msaa139

[3] Yasamin Tabatabaee, Chao Zhang, Tandy Warnow, Siavash Mirarab, Phylogenomic branch length estimation using quartets, Bioinformatics, Volume 39, Issue Supplement_1, June 2023, Pages i185–i193, https://doi.org/10.1093/bioinformatics/btad221

Example of usage

We obtained the species tree from muti-copy gene family trees using ASTRAL-Pro3 v1.19.3.5 [1] by optimizing the objective function of ASTRAL-Pro [2]. Branch lengths are computed using integrated CASTLES-Pro [3].

Announcements

Integrated in Phylosuite (NEW)

Many ASTER tools have been integrated in PhyloSuite, an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies.

GUI for Windows users

Please check out our software with GUI. Simply download the zip file, extract the contents, enter exe folder, and click aster-gui.exe.

Bug Reports

Contact chaozhang@berkeley.edu, aster-users@googlegroups.com, or post on ASTER issues page.

Documentations

INSTALLATION

For most users, installing ASTER is very easy! Download using one of two approaches:

  • You simply need to download the zip file for Windows/MacOS/Linux and extract the contents to a folder of your choice.
  • Alternatively, you can clone the github repository and checkout the branch named Windows/MacOS/Linux.

Binary files should be in the exe folder for Windows or bin folder otherwise. If you are lucky, these may just work as is and you may not need to build at all.

For Linux/Unix/WSL users

  1. In terminal, cd into the downloaded directory and run make.
  • If you see *** Installation complete! *** then you are done!
  • If you see Command 'g++' not found then before rerunning make,
    • Debian (Ubuntu) users try 
      sudo apt update
sudo apt install g++
    • CentOS (RedHat) users try 
      sudo yum update
sudo yum install gcc-c++
    • Unix (MacOS) users should be prompted for installing g++ and please click "install". If no prompt, try g++.
  • If you see "error" when running make, please try make astral-pro3 instead and file a bug report.
  1. Binary files should be in the bin folder.

For Windows users

  • Executables for x86-64 are available in exe folder and it is very likely that they already work.
  • Windows Subsystem for Linux (WSL) is HIGHLY recommanded if you need to install on your own! Please follow instructions in "For Linux/Unix/WSL users" section.
  • To compile windows excutables:
    1. Download MinGW and install posix version for your architecture (eg. x86-64)
    2. Add path to bin folder of MinGW to system environment variable PATH
    3. Double click make.bat inside the downloaded directory

GUI for Windows users (NEW)

Please check out our software with GUI. Simply download the zip file, extract the contents, enter exe folder, and click aster-gui.exe.

INPUT

  • The input gene trees are in the Newick format
  • The input trees can have missing taxa, polytomies (unresolved branches), and multi-copy genes.
  • When multiple genes from the same species are available, you can ask ASTRAL to force them to be together in the species tree. You can do this in two ways.
    1. You can give multiple genes from the same species the same name in the input gene trees (e.g., ((species_name_A,species_name_B),(species_name_A,species_name_C));).
    2. OR, a mapping file needs to be provided using the -a option. This mapping file should have one line per genes, and each line needs to be in the following formats (e.g., for gene trees like ((gene_A1,gene_B1),(gene_A2,gene_C1));):
gene_A1 species_name_A
gene_A2 species_name_A
gene_B1 species_name_B
gene_B2 species_name_B
gene_B3 species_name_B
...

OUTPUT

The output in is Newick format and gives:

  • the species tree topology
  • (NEW) branch lengths in substitution-per-site units (IQ-TREE like) for all branches
  • branch supports measured as local posterior probabilities
  • It can also annotate branches with other quantities, such as quartet supports and localPPs for all three topologies.

EXECUTION

ASTER currently has no GUI. You need to run it through the command-line. In a terminal/PowerShell, go to the directory (location) where you have downloaded ASTER and issue the following command:

bin/astral-pro3

This will give you a list of options available. If you are using Windows, please replace bin/astral-pro3 with .\exe\astral-pro3.exe.

To find the species tree with input from in a file called INPUT_FILE, use:

bin/astral-pro3 INPUT_FILE

or

bin/astral-pro3 -i INPUT_FILE

In the first case, INPUT_FILE is hard-coded to be the last argument for backward compatibility.

For example if you want to run astral-pro3 with input example/multitree.nw, then run

bin/astral-pro3 example/multitree.nw

or

bin/astral-pro3 -i example/multitree.nw

The results will be outputted to the standard output. To save the results in a file use the -o OUTPUT_FILE option before INPUT_FILE(Strongly recommended):

bin/astral-pro3 -o OUTPUT_FILE INPUT_FILE

or

bin/astral-pro3 -i INPUT_FILE -o OUTPUT_FILE

With -i INPUT_FILE option, the order does not matter anymore. For brevity, from here on we will not demonstrate -i INPUT_FILE cases.

To save the logs (also recommended), run:

bin/astral-pro3 -o OUTPUT_FILE INPUT_FILE 2>LOG_FILE

For example, you can run

bin/astral-pro3 -o example/multitree.nw.stree example/multitree.nw 2>example/multitree.nw.log

ASTER supports multi-threading. To run program with 4 threads, add -t 4 before INPUT_FILE:

bin/astral-pro3 -t 4 -o OUTPUT_FILE INPUT_FILE 2>LOG_FILE

ASTER has very good parrallel efficiency up to 64 cores when input data is large. In fact, it often experiences super-linear speedup with 16 cores or more. So feel free to use as many cores as you want.

ASTER also allows rooting at an given outgroup:

bin/astral-pro3 --root YOUR_OUTGROUP INPUT_FILE

For ASTRAL-Pro, correct rooting is strongly recommended to accurately compute branch lengths.

By default, ASTRAL-Pro assumes multiple genes from the same species in the same input gene trees having the same name. Alternatively, a mapping file needs to be provided using the -a option (see INPUT section). For example,

bin/astral-pro3 -a example/multitree_genename.map example/multitree_genename.nw

Advanced Options

ASTER algorithm first performs R (4 by default) rounds of search and then repeatedly performs S (4 by default) rounds of subsampling and exploration until no improvement found.

bin/astral-pro3 -r R -s S -o OUTPUT_FILE INPUT_FILE 2>LOG_FILE

If you want to run with more rounds of placement for ensured optimality, then you can run with

bin/astral-pro3 -r 16 -s 16 -o OUTPUT_FILE INPUT_FILE 2>LOG_FILE

or simply

bin/astral-pro3 -R -o OUTPUT_FILE INPUT_FILE 2>LOG_FILE

If you want to place taxa on an existing fully resolved species tree, you can use -c SPECIES_TREE_IN_NEWICK_FORMAT before INPUT_FILE:

bin/astral-pro3 -o OUTPUT_FILE -c SPECIES_TREE_IN_NEWICK_FORMAT INPUT_FILE

Specifically, you can score and annotate a fully resolved species tree containing all taxa with -c SPECIES_TREE_IN_NEWICK_FORMAT. If want to score a species tree or you want to place only one taxon onto the tree, you can use

bin/astral-pro3 -r 1 -s 0 -o OUTPUT_FILE -c SPECIES_TREE_IN_NEWICK_FORMAT INPUT_FILE

or simply,

bin/astral-pro3 -C -o OUTPUT_FILE -c SPECIES_TREE_IN_NEWICK_FORMAT INPUT_FILE

If you want to give hints by providing candidate species trees or trees similar to the species tree, you can use -g SPECIES_TREES_IN_NEWICK_FORMAT before INPUT_FILE:

bin/astral-pro3 -o OUTPUT_FILE -g SPECIES_TREES_IN_NEWICK_FORMAT INPUT_FILE

Add -u 0 before INPUT_FILE if you want to compute species tree topology only; Add -u 2 before INPUT_FILE if you support and local-PP for all three resolutions of each branch.

bin/astral-pro3 -u 0 -o OUTPUT_FILE INPUT_FILE
bin/astral-pro3 -u 2 -o OUTPUT_FILE INPUT_FILE

Species tree with more than 5000 taxa may cause overflow. Use the following command instead:

make astral-pro_int128
bin/astral-pro3_int128 -o OUTPUT_FILE INPUT_FILE

If you do not want to compute optimal species tree but instead just want to root and tag gene trees, you can use the following command:

bin/astral-pro3 -T -o OUTPUT_FILE INPUT_FILE