seq-gen has limited model set. sowhat needs to check models before any processes are run. about sowhat HOT 1 CLOSED

Model checks were integrated previously. The available models are listed below. Specifying any other models should return this error at the outset.
sowhat recognizes the following models:
nucleotide data:
- RAxML models - GTRGAMMA[I|X] GTRCAT[I|X]
(CAT model will not be used for simulation)
- GARLI models - all options except fixed
amino acid data:
- RAxML models - PROTGAMMA[I|X]... PROTCAT[I|X]
(CAT model will not be used for simulation)
matrices: JTT WAG DAYHOFF BLOSUM62 MTREV CPREV45 GTR GTR_UNLINKED
- GARLI models - all options except fixed
matrices: JONES WAG DAYHOFF MTREV MTMAM
character data:
- RAxML models - MULTIGAMMA[I|X] MULTICAT[I|X]
anywhere from 2 - 20 character states are supported
characters must be used in this order as they are available
0 1 2 3 4 5 6 7 8 9 A B C D E F G H I J
these will be resorted from most to least freq. in simulations
many low frequency character states will return a raxml error
(CAT model will not be used for simulation)
- GARLI + character data is currently not available
alternative options:
- The PhyloBayes CAT_GTR model can be used for parameter
estimation and data simulation w/ --usepb
- A user specified model can be used for simulation w/ --usegenmodel
see example file examples/simulation.model
- The user can specify the --max option to maximize free
parameters used in simulation

from sowhat.