Alignment
Filename:
Alignment type
nucleotide
amino acid
codon (one-letter code)
Code table
Universal
Mitochondrial
Initial tree in newick format
None
From file:
Method
Amino Acid substitution model
Equilibrium frequencies:
equal to frequencies in sequences
to be optimized
Variation oversites
None
Substitution rates
Discrete Gamma:
4 categories
8 categories
Initial values for alpha(shape parameter):
To be Optimized:
yes
no
Options:
Amino Acid exchangeabilities:
JTT
WAG
LG
KHGaa
mtREV
cpREV10
cpREV64
Use Codon substitution model
Codon substitution model
Equilibrium frequencies:
equal to frequencies in sequences
to be optimized
From file
Variation oversites
None
Substitution rates
Selective constraints
Discrete Gamma:
4 categories
8 categories
Initial values for alpha(shape parameter):
Default
To be Optimized:
yes
no
Selective Constraints on Amino Acids:
EI
JTT-ML91+
WAG-ML91+
LG-ML91+
KHG-ML200
No-Constraint
ML parameters:
1
5
8
12
1
4
7
11
12
Initial values for parameters:
for nuclear genes
for cpDNA
for mtDNA
default values
as follows
Probability of neutral substitution between amino acids a and b:
exp(βw(a,b) + w
0
(1-δab))
β
Default
w
0
Default
Scale parameter of Gamma distribution:
Default
initial values of nucleotide exchangeabilities [m
ij
]:
ratio (m) of double/triple to single/double nucleotide changes:
Default
m
tc|ag
/ m
[tc][ag]
:
Default
m
ag
/ m
tc[ag]
:
Default
m
ta
/ m
[tc][ag]
:
Default
m
tg
/ m
[tc][ag]
:
Default
m
ca
/ m
[tc][ag]
:
Default
initial values of nucleotide equilibrium frequencies [f
i
]:
f
a
:
Default
f
c
:
Default
f
g
:
Default
Optimize tree
yes
no