AU test on each bipartition

Technical documents are here.

• Citation
• Dependencies
• Installation
  • By Singularity
  • Without Singularity
    • Linux
    • Windows
• Usage
  • By Singularity
  • Without Singularity
    • Linux
    • Windows
  • Options
    • General options
    • IQ-TREE options
    • CONSEL options
    • Output options
  • Examples of usage
• Output

Bamba K., Harada R., Inagaki Y. (2024) AUTOEB: A Software for Systematically Evaluating Bipartitions in a Phylogenetic Tree Employing an Approximately Unbiased Test. IPSJ Transactions on Bioinformatics, 17: 72–82.

DOI: 10.2197/ipsjtbio.17.72

• Python
  • version: 3.11
  • web site: https://www.python.org/
• IQ-TREE
  • version: 2.2.0
  • web site: http://www.iqtree.org/
  • GitHub: https://github.com/iqtree/iqtree2
  • citation: B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeseler, R. Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., 37:1530-1534. doi: 10.1093/molbev/msaa015
• CONSEL
  • version: commit at 1a532a4fe9e7d4e9101f2bbe64613f3b0cfc6274
  • web site: http://stat.sys.i.kyoto-u.ac.jp/prog/consel/
  • GitHub: https://github.com/shimo-lab/consel
  • citation: Shimodaira H., Hasegawa M. (2001). CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics. Dec;17(12):1246-7. doi: 10.1093/bioinformatics/17.12.1246.

Whichever installation type you select, you have to clone this repository in advance. DO NOT use the main branch for installation. You should checkout the tag associated with target version of this software (In git clone command, -b TAG option is usable).

git clone [email protected]:MEMlabo/AUTOEB.git -b v1.1.1

To build singularity container, execute scripts/build-singularity.sh. When the build successes, the container file autoeb.sif is created at package/.

chmod +x ./scripts/build-singularity.sh
bash ./scripts/build-singularity.sh

At first, execute scripts/init.sh to initialize the project.

chmod +x ./scripts/init.sh
bash ./scripts/init.sh

Next, add package path of autoeb to .bashrc by using the environment variant PYTHONPATH.

Example of .bashrc

export PYTHONPATH=$PYTHONPATH:<repo dir>/src/

Lastly, set the command to execute IQ-TREE and path of CONSEL by modifying src/autoeb/config.json.

Example of config.json

{
    "iqtree_command": "iqtree2.2.0",
    "consel_dir": "/usr/local/bin/"
}

At first, execute scripts/init.ps1 to initialize the project.

.\scripts\init.ps1

Next, add package path of autoeb by using the variant PYTHONPATH (Using control panel is easy way).

Lastly, set the command to execute IQ-TREE and path of CONSEL by modifying src/autoeb/config.json.

Example of config.json

{
    "iqtree_command": "iqtree2.exe",
    "consel_dir": "$PATH"
}

Use singularity run command to execute.

singularity run ./package/autoeb.sif <parameters>

Execute scripts/exec_autoeb.sh.

bash ./scripts/exec_autoeb.sh <parameters>

Execute scripts/exec_autoeb.ps1.

.\scripts\exec_autoeb.ps1 <parameters>

When specify --iqtree-param option, specify a text file which represents parameters to give in running IQ-TREE. In loading the text file, new line (\n) is replaced by white space.

autoeb -s seq.fasta -t ml.tree -m LG+F+G -o autoeb --iqtree-param iqtree-parameters.txt

--mem 100G
--safe

In the most common use case of AUTOEB, sequence file seq.fasta and tree file ml.treefile are specified files. LG+C60+F+G is specified as substitution model. Output files are contained at output_autoeb directory.

singularity run autoeb.sif -s seq.fasta -t ml.treefile -m LG+C60+F+G -o output_autoeb

-T option specifies the number of threads used. See also here.

singularity run autoeb.sif -s seq.fasta -t ml.treefile -m LG+C60+F+G -T 16 -o output_autoeb

See here.