Weighted ASTRAL program has the following modes for different weighting schemes:

1. Weighted ASTRAL by Branch Support (mode 2)
2. Weighted ASTRAL by Branch Length (mode 3)
3. Weighted ASTRAL - Hybrid (default)

Weighted ASTRAL series introduce threshold-free weighting schemes for the quartet-based species tree inference, the metric used in the popular method ASTRAL. By reducing the impact of quartets with low support or long terminal branches (or both), weighting provides stronger theoretical guarantees and better empirical performance than the unweighted ASTRAL. Our results show that weighted ASTRAL improves the utility of summary methods and can reduce the incongruence often observed across analytical pipelines.

Publication

[1] Chao Zhang, Siavash Mirarab, Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees, Molecular Biology and Evolution, 2022, msac215, https://doi.org/10.1093/molbev/msac215

Example of usage

We obtained the species tree from gene trees using wASTRAL v1.25.4.8 [1].

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@pku.edu.cn, aster-users@googlegroups.com, or post on ASTER issues page.

Documentations

• The rest of this TUTORIAL file
• Forums (feel free to ask questions or ask for help running ASTER):
  • User group discussions
  • ASTER issues page
  • QQ group: 130635706

INSTALLATION

For most users, installing ASTER is very easy! Install using one of three approaches:

• You simply need to download the zip file for Windows/MacOS ARM/MacOS X86/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.
• For MacOS/Linux users, you can also install ASTER using conda:

  conda install aster
  

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/MacOS/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++. Please ensure that Clang version is at least 14.
• If you see "error" when running make, please try make wastral instead and file a bug report.

2. 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 multiple individuals/genes per species.
• When individuals/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 individuals/genes from the same species the same name in the input gene trees.
  2. OR, a mapping file needs to be provided using the -a option.

individual_A1 species_name_A
individual_A2 species_name_A
individual_B1 species_name_B
individual_B2 species_name_B
individual_B3 species_name_B
...

Or

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
...

1. Weighted ASTRAL by Branch Support (mode 2): Non-root interal node labels must be a non-negative number being support. Eg. ((A,B)100,(C,D)0); or ((A:1,B:1)1.0:1,(C:1,D:1)0.333:0);.
2. Weighted ASTRAL by Branch Length (mode 3): Non-root labels must have branch lengths after :. Eg. ((A,B):1,(C,D):0); or ((A:1,B:1)1.0:1,(C:1,D:1)0.333:0);.
3. Weighted ASTRAL - Hybrid (default): Non-root interal node labels must be a non-negative number being support before : and non-root labels must have branch lengths after :. Eg. ((A:1,B:1)100:1,(C:1,D:1)0:0); or ((A:1,B:1)1.0:1,(C:1,D:1)0.333:0);.

OUTPUT

The output in is Newick format and gives:

• the species tree topology
• branch lengths in coalescent units for astral-weighted and in combined (coalensecent + 2 * substitution) units (only for internal 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.

The weighted ASTRAL tree leaves the branch length of terminal branches empty. Some tools for visualization and tree editing do not like this (e.g., ape). In FigTree, if you open the tree several times, it eventually opens up (at least on our machines). In ape, if you ask it to ignore branch lengths all together, it works. In general, if your tool does not like the lack of terminal branches, you can add a dummy branch length, as in this script.

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/wastral

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

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

bin/wastral INPUT_FILE

or

bin/wastral -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 wastral with input example/genetree.nw, then run

bin/wastral example/genetree.nw

or

bin/wastral -i example/genetree.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/wastral -o OUTPUT_FILE INPUT_FILE

or

bin/wastral -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/wastral -o OUTPUT_FILE INPUT_FILE 2>LOG_FILE

For example, you can run

bin/wastral -o example/genetree.nw.stree example/genetree.nw 2>example/genetree.nw.log

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

bin/wastral -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/wastral --root YOUR_OUTGROUP INPUT_FILE

By default, wASTRAL assumes multiple individuals/alleles 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/wastral -a example/genetree.map example/genetree.nw

When your dataset has no more than 50 species and no more than 500 genes, you may want to run with more rounds using -R (see below).

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/wastral -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/wastral -r 16 -s 16 -o OUTPUT_FILE INPUT_FILE 2>LOG_FILE

or simply

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

or simply,

bin/wastral -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/wastral -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/wastral -u 0 -o OUTPUT_FILE INPUT_FILE
bin/wastral -u 2 -o OUTPUT_FILE INPUT_FILE

Species tree with more than 2000 taxa may cause floating point underflow or precision issue. Use the following command instead:

make wastral_precise
bin/wastral_precise -o OUTPUT_FILE INPUT_FILE

Notice: For hybrid weighting (default) and weighting by support (mode 2), wASTRAL by default will automatically detect support type. You may also specify max (-x) and min (-n) of support value to the program.

bin/wastral -x MAX_SUPPORT -n MIN_SUPPORT INPUT_FILE

For Bootstrap support, any of the following commands works:

bin/wastral -S INPUT_FILE
bin/wastral -x 100 -n 0 INPUT_FILE

For local Baysian support, -x 1 -n 0.333 is recommended or -B for short:

bin/wastral -B INPUT_FILE

or

bin/wastral -x 1 -n 0.333 INPUT_FILE

For other probability & likelihood support, -x 1 -n 0 may be more reasonable or -L for short:

bin/wastral -L INPUT_FILE

or

bin/wastral -x 1 -n 0 INPUT_FILE

By default, wASTRAL assumes multiple individuals/alleles 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/wastral -a example/genetree.map example/genetree.nw

In case you want to run Weighted ASTRAL by Branch Support, you can do:

bin/wastral --mode 2 -o OUTPUT_FILE INPUT_FILE

In case you want to run Weighted ASTRAL by Branch Length, you can do:

bin/wastral --mode 3 -o OUTPUT_FILE INPUT_FILE