V.S.D.S. Mahesh Akavarapu, Arnab Bhattacharya
Runs on Linux 64-bit
The datafiles are present in data/. Pip requirements are in requirements.txt.
Note that all the test is run on various the families and methods in parallel, hence make sure that resources are sufficient.
Tested on 12 core CPU 3.2 GHz and 32 GB RAM
The programs re-run only if the relavent result files are missing. We provide all of them beforehand. If one wishes to re-run from scratch clear the directory results/ and run the experiments.
To generate the results for LRT saved in results/lrt_<family>.json, run the following command (should take less an hour):
python run_lrt.py
To generate the results for multilateral permutation tests, run the following command (Should take about 8 hrs):
python run_nos.py
Individual families and methods can be tested by the running run_perm_test.py, run the following command for help:
python run_perm_test.py --help
To generate the results for tree construction task, run the following command (should take about 8 hrs):
python run_test_trees.py
This command, however does not generate ML-trees, they have to be manually generated on the alignment files generated by src/align.py at processed/aligned/,
on the families test_aa, test_an, test_ie, test_pn and test_st
For example, for family test_aa, run python src/align.py test_aa and then manually analyze maximum likelihood tree from processed/aligned/test_aa_dolgo.fa
by using MEGA11 GUI (install from here) and the model POISSON+I+G2 by NNI search (fastest) and save the Newick tree as results/test_aa_ml.tre
Once all the required files are generated, the results can be tabulated by running:
python tabulate_res.py
The results are tabulated in results/summary_<task>.tsv. The primary results as well as those for evaluation of macro-families are generated together.ho
Analysis on Nostratic is performed manually using the .fa files from processed/aligned/ on MEGA11 GUI with model Poisson+I.