This repository contains Python code for calculating likelihood (lkl) for phylogenetic trees. The code includes two main functionalities:
-
Get LKL for All Nodes:
python3 run_lkl_calculation.py \ --tree_path data/table.dat \ --branch_lengths_path data/branchlength.dat \ --msa_path data/msa.dat \ --mu 1
-
Get LKL for Root Node Only:
python3 run_lkl_calculation.py \ --tree_path data/table.dat \ --branch_lengths_path data/branchlength.dat \ --msa_path data/msa.dat \ --mu 1 \ --output_lkl_root_node_only
To run the test datasets, you can use the following commands:
# Install required dependencies
pip install tabulate
# Run the test script
python3 test.py
## Output of test script
+-----------------------------------+--------+-------------------+-----------------+----------------+
| Dataset | Mu | Expected Output | Actual Output | Match Status |
+===================================+========+===================+=================+================+
| msa.dat | 0.3 | -180.431 | -180.431 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+
| msa.dat | 1 | -182.056 | -182.056 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+
| msa.dat | 2 | -197.3 | -197.3 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+
| msa.dat | 0.5321 | -176.507 | -176.507 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+
| ENSG00000112282_MED23_NT.msa.dat | 0.3 | -11350.6 | -11350.6 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+
| ENSG00000112282_MED23_NT.msa.dat | 1 | -10229.9 | -10229.9 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+
| ENSG00000112282_MED23_NT.msa.dat | 2 | -10534.2 | -10534.2 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+
| ENSG00000112282_MED23_NT.msa.dat | 1.1549 | -10211.9 | -10211.9 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+
| ENSG00000112984_KIF20A_NT.msa.dat | 0.3 | -7412.28 | -7412.28 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+
| ENSG00000112984_KIF20A_NT.msa.dat | 1 | -7134.62 | -7134.62 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+
| ENSG00000112984_KIF20A_NT.msa.dat | 2 | -8029.3 | -8029.3 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+
| ENSG00000112984_KIF20A_NT.msa.dat | 0.7021 | -7043.94 | -7043.94 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+
| ENSG00000013016_EHD3_NT.msa.dat | 0.3 | -6802.54 | -6802.54 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+
| ENSG00000013016_EHD3_NT.msa.dat | 1 | -7324.27 | -7324.27 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+
| ENSG00000013016_EHD3_NT.msa.dat | 2 | -9147.93 | -9147.93 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+
| ENSG00000013016_EHD3_NT.msa.dat | 0.4242 | -6737.3 | -6737.3 | Match |
+-----------------------------------+--------+-------------------+-----------------+----------------+