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Without-Alignment/Assembly Species Tree EstimatoR † (WASTER)

WASTER is a coalesence-aware de novo species tree inference tool, which means it can take as inputs raw reads in FASTQ format. Paticularly, WASTER can accurately infer species tree even from Illumina reads with only 1.5X depth. WASTER infers the species tree by first calling SNPs from reads/assembies and then invoking CASTER to reconstruct the species tree from the SNPs.

Publication

TBA

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 [email protected], [email protected], 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 waster-site 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.

STOP!

If you have overlapping paired-end sequencing reads, please make sure you have merged them using BBMerge or alike. This will improve the accuracy of WASTER on biological datasets! If you have non-overlapping paired-end sequencing reads, great! With the same sequencing depth, WASTER prefers non-overlapping reads.

INPUT

The input is a text file containing a list of species names each followed by a Fasta/Fastq file (one species name and one file per line). For example:

speciesA	example/waster/filename1.fa
speciesB	example/waster/filename2.fa
speciesC	example/waster/filename3.fq
speciesD	example/waster/filename4.fq

Make sure input files are not zipped.

When multiple individuals from the same species are available, you need to let WASTER to know that they are from the same species.

  1. You can give multiple individuals from the same species the same name in the input list.
speciesA	example/waster/filename1.fa
speciesA	example/waster/filename2.fa
speciesB	example/waster/filename3.fq
speciesB	example/waster/filename4.fq
...

WARNING: Never use this method to input pair-end reads files!!! If your pair-end reads overlap, then merge them using BBMerge or alike; otherwise cat them into one file.

OUTPUT

The output in is Newick format and gives:

  • the species tree topology
  • branch supports measured as local bootstrap support (>95.0 means good)
  • It can also annotate branches with other quantities, such as quartet scores and local bootstraps 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/waster-site

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

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

bin/waster-site INPUT_FILE

or

bin/waster-site -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 waster-site with input example/waster/input_list.txt, then run

bin/waster-site example/waster/input_list.txt

or

bin/waster-site -i example/waster/input_list.txt

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/waster-site -o OUTPUT_FILE INPUT_FILE

or

bin/waster-site -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/waster-site -o OUTPUT_FILE INPUT_FILE 2>LOG_FILE

For example, you can run

bin/waster-site -o example/waster/input_list.txt.stree example/waster/input_list.txt 2>example/waster/input_list.txt.log

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

bin/waster-site -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/waster-site --root YOUR_OUTGROUP INPUT_FILE

Notice: By default, WASTER will create a 32 GB look-up table to find SNPs. So, if you are running on a machine with <64 GB memory, you need to shrink the look-up table size using -k 8 or -k 7 even for the example run. Using -k 8 requires about 4 GB memory and -k 7 only requires <1 GB memory. Try the following example run:

bin/waster-site -k 7 example/waster/input_list.txt

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/waster-site -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/waster-site -r 16 -s 16 -o OUTPUT_FILE INPUT_FILE 2>LOG_FILE

or simply

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

or simply,

bin/waster-site -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/waster-site -o OUTPUT_FILE -g SPECIES_TREES_IN_NEWICK_FORMAT INPUT_FILE