#JC
datatype = nucleotide
ratematrix = 1rate
statefrequencies = equal
ratehetmodel = none
numratecats = 1
invariantsites = none

#JC+I
datatype = nucleotide
ratematrix = 1rate
statefrequencies = equal
ratehetmodel = none
numratecats = 1
invariantsites = estimate

#JC+G
datatype = nucleotide
ratematrix = 1rate
statefrequencies = equal
ratehetmodel = gamma
numratecats = 4
invariantsites = none

#JC+I+G
datatype = nucleotide
ratematrix = 1rate
statefrequencies = equal
ratehetmodel = gamma
numratecats = 4
invariantsites = estimate

#F81
datatype = nucleotide
ratematrix = 1rate
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = estimate

#F81+I
datatype = nucleotide
ratematrix = 1rate
statefrequencies = estimate
ratehetmodel = none
numratecats = 1
invariantsites = estimate

#F81+G
datatype = nucleotide
ratematrix = 1rate
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = none

#F81+I+G
datatype = nucleotide
ratematrix = 1rate
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = estimate

#K80
datatype = nucleotide
ratematrix = 2rate
statefrequencies = equal
ratehetmodel = none
numratecats = 1
invariantsites = estimate

#K80+I
datatype = nucleotide
ratematrix = 2rate
statefrequencies = equal
ratehetmodel = none
numratecats = 1
invariantsites = estimate

#K80+G
datatype = nucleotide
ratematrix = 2rate
statefrequencies = equal
ratehetmodel = gamma
numratecats = 4
invariantsites = none

#K80+I+G
datatype = nucleotide
ratematrix = 2rate
statefrequencies = equal
ratehetmodel = gamma
numratecats = 4
invariantsites = estimate

#HKY
datatype = nucleotide
ratematrix = 2rate
statefrequencies = estimate
ratehetmodel = none
numratecats = 1
invariantsites = none

#HKY+I
datatype = nucleotide
ratematrix = 2rate
statefrequencies = estimate
ratehetmodel = none
numratecats = 1
invariantsites = estimate

#HKY+G
datatype = nucleotide
ratematrix = 2rate
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = none

#HKY+I+G
datatype = nucleotide
ratematrix = 2rate
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = estimate

#SYM
datatype = nucleotide
ratematrix = 6rate
statefrequencies = equal
ratehetmodel = none
numratecats = 1
invariantsites = none

#SYM+I
datatype = nucleotide
ratematrix = 6rate
statefrequencies = equal
ratehetmodel = none
numratecats = 1
invariantsites = estimate

#SYM+G
datatype = nucleotide
ratematrix = 6rate
statefrequencies = equal
ratehetmodel = gamma
numratecats = 4
invariantsites = none

#SYM+I+G
datatype = nucleotide
ratematrix = 6rate
statefrequencies = equal
ratehetmodel = gamma
numratecats = 4
invariantsites = estimate

#GTR
datatype = nucleotide
ratematrix = 6rate
statefrequencies = estimate
ratehetmodel = none
numratecats = 1
invariantsites = none

#GTR+I
datatype = nucleotide
ratematrix = 6rate
statefrequencies = estimate
ratehetmodel = none
numratecats = 1
invariantsites = estimate

#GTR+G
datatype = nucleotide
ratematrix = 6rate
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = none

#GTR+I+G
datatype = nucleotide
ratematrix = 6rate
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = estimate

#TVM
datatype = nucleotide
ratematrix = (0 1 2 3 1 4) 
statefrequencies = estimate
ratehetmodel = none
numratecats = 1
invariantsites = none

#TVM+I
datatype = nucleotide
ratematrix = (0 1 2 3 1 4) 
statefrequencies = estimate
ratehetmodel = none
numratecats = 1
invariantsites = estimate

#TVM+G
datatype = nucleotide
ratematrix = (0 1 2 3 1 4) 
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = none

#TVM+I+G
datatype = nucleotide
ratematrix = (0 1 2 3 1 4) 
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = estimate

#TrN
datatype = nucleotide
ratematrix = (0 1 0 0 1 0)
statefrequencies = estimate
ratehetmodel = none
numratecats = 1
invariantsites = none

#TrN+I
datatype = nucleotide
ratematrix = (0 1 0 0 1 0)
statefrequencies = estimate
ratehetmodel = none
numratecats = 1
invariantsites = estimate

#TrN+G
datatype = nucleotide
ratematrix = (0 1 0 0 1 0)
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = none

#TrN+I+G
datatype = nucleotide
ratematrix = (0 1 0 0 1 0)
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = estimate

#K81uf
datatype = nucleotide
ratematrix = (0 1 2 2 1 0)
statefrequencies = estimate
ratehetmodel = none
numratecats = 1
invariantsites = none

#K81uf+I
datatype = nucleotide
ratematrix = (0 1 2 2 1 0)
statefrequencies = estimate
ratehetmodel = none
numratecats = 1
invariantsites = estimate

#K81uf+G
datatype = nucleotide
ratematrix = (0 1 2 2 1 0)
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = none

#K81uf+I+G
datatype = nucleotide
ratematrix = (0 1 2 2 1 0)
statefrequencies = estimate
ratehetmodel = gamma
numratecats = 4
invariantsites = estimate

