- Version: 0.2
python3 setup.py install # Installation
python3 setup.py test # Testing
or
pip install git+https://github.com/Yanjo96/FAAUTeC.git
- 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
For a correct run I would recommend to specify the complete paths.
-
--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
-
--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
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
The program does not work on Windows currently.
- Check requirements
- (Windows support)