AUTOEB

AU test on each bipartition

Technical documents are here.

Index

• 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

Citation

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

Dependencies

• 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.

Installation

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

By Singularity

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

Without Singularity

Linux

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/"
}

Windows

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"
}

Usage

By Singularity

Use singularity run command to execute.

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

Without Singularity

Linux

Execute scripts/exec_autoeb.sh.

bash ./scripts/exec_autoeb.sh <parameters>

Windows

Execute scripts/exec_autoeb.ps1.

.\scripts\exec_autoeb.ps1 <parameters>

Options

General options

Name	Full Name	Type / Default	Required	Description
-h	--help	flag	-	Show the help of this application
-v	--version	flag	-	Show the version of this application
-s	--seq	file	+	Path of sequences (file format should be applicable for IQ-TREE)
-t	--tree	file	+	Path of ML-tree file
	--range	string / ALL	-	Specifies which bipartition to analyze e.g.) ALL (all bipartitions), -5 (0th to 5th) ,3-11 (3rd to 11th), 4,13- (4th and 13th to last bipartition)
	--sig-level	float (0 < value < 1) / 0.05	-	Significance level of rejecting NNI-tree
-T	--thread	int (>=1) / 1	-	Specifies the number of threads used in IQ-TREE and parallel execution of CONSEL
	--redo	flag	-	Ignore checkpoints and force to execute all operation

IQ-TREE options

Name	Full Name	Type / Default	Required	Description
-m	--model	string	+	Substitution model supported by IQ-TREE e.g.) LG+I+G, WAG+C20+F+R10
	--iqtree-param	file / null	-	The text file with optional parameters used in executing IQ-TREE
-b	--bootstrap	int (>= 1000) /100,000	-	Specifies the number of replicates by RELL-bootstrap in makermt (in CONSEL package)
	--iqtree-verbose	flag	-	IQ-TREE log become redirected to stdout.

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.

Example

AUTOEB Command:

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

iqtree-parameters.txt:

--mem 100G
--safe

CONSEL options

Name	Full Name	Type / Default	Required	Description
	--seed	int (>= 0) / -1	-	Specifies the seed of RELL-bootstrap by the makermt. If 0, system time is used for seed (each bipartition has different values). If -1 (default), random value is used (each bipartition has the same value)

Output options

Name	Full Name	Type / Default	Required	Description
-o	--out	directory	+	Directory to output files. If specified directory doesn't exist, created automatically
-f	--out-format	string / {src}/{bin}	-	Specifies the format of bipartitions. See also here
	--output-tmp-files	flag	-	All temporary files are retained and compressed into tmp-output.tar.gz.

Examples of usage

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

Output

See here.