faautec's Introduction

FAAUTeC: Fully Automated Approximately Unbiased Test Comparer

Version: 0.2

INSTALLATION

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

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