The current hardcoded usage of TreeTime in augur refine is to instantiate the JC69 substitution model and then to re-estimate the parameters (infer_gtr=True). PR #1958 will change this to use the JTT92 model for AA sequences.
It does seem a little strange to use a different model in augur tree (GTR by default) than in refine, but for short branches it's probably fine. Note that augur ancestral, when reconstructing AA sequences, uses JTT92 (with 22 (?) states).
In review @joverlee521 asks if we should expose a --gtr argument to augur refine?
The current hardcoded usage of TreeTime in
augur refineis to instantiate theJC69substitution model and then to re-estimate the parameters (infer_gtr=True). PR #1958 will change this to use theJTT92model for AA sequences.It does seem a little strange to use a different model in
augur tree(GTR by default) than in refine, but for short branches it's probably fine. Note thataugur ancestral, when reconstructing AA sequences, usesJTT92(with 22 (?) states).In review @joverlee521 asks if we should expose a
--gtrargument to augur refine?