sate-dev/sate-core — Issue #1: Reading likelihood from RAxML_info
Author: smirarab
Created: 2011-10-18 19:42:55+00:00
State: open

Currently the likelihood score is read from RAxML_log file. When MIX model is used (or if CAT model is used and RAxML version is 7.2.8) after the tree space is searched using CAT, a final round of model parameter optimization occurs under GAMMA.

The result from this final GAMMA-based round is not reported in RAxML_log file. Instead the results are reported in RAxML_info file. Function read_raxml_results from tools.py needs to change to read the likelilhood from the RAxML_info file instead of the log file.

Thanks
Siavash