FAAUTeC: Fully Automated Approximately Unbiased Test Comparer

• Version: 0.2

INSTALLATION

python3 setup.py install  # Installation
python3 setup.py test     # Testing

or

pip install git+https://github.com/Yanjo96/FAAUTeC.git

Requirements

• RAxML (https://github.com/stamatak/standard-RAxML)
• CONSEL (http://stat.sys.i.kyoto-u.ac.jp/prog/consel/)
• IQTree (http://www.iqtree.org/)
• Python3
• Biopython
• Dendropy
• Optional: ete3
• Optional: xelatex
• Optional: IQTree2 (http://www.iqtree.org/)

Don't forget to give all programs the permission to be executed

USAGE

For a correct run I would recommend to specify the complete paths.

Parameters

Mandatory

• --alignment | -a
  absolute path to infile; infile in PHYLIP or FASTA format; Example: /path_to_input/test.phy

• --constraint| -c
  absolute path to constraint file; infile in NEWICK format; Example: /path_to_input/tree.tre

Optional

• --model
  Model for RAxML

• --ml_inference
  Choose which program should run the ML-Tree calculation 'RAxML' or 'IQTree'

• --path_iqtree
  absolute path to the iqtree executable

• --path_raxml
  absolute path to the RAxML executable

• --au_inference
  Choose program for AU-test calculation 'CONSEL' or 'IQTree' or 'IQTree2', multiple selection possible by ';' as delimiter, e.g. 'CONSEL;IQTree'

• --path_consel
  path to consel executables

• --path_iqtree2
  absolute path to the iqtree2 executable

• --latex_format
  Creates a more beautiful Table with xelatex

• --thread_number
  Number of maximal used threads

• --version
  print version number and exit

On Linux

ALIGN=examples/input/FASTA/
CONST=examples/input/Constraint/tree_hypothesis.txt
CONSL=path/to/consel

FAAUTeC -a $ALIGN -c $CONST --ml_inference "RAxML" --au_inference "CONSEL" --path_consel $CONSL

On Windows

The program does not work on Windows currently.

TODO

• Check requirements
• (Windows support)