Alignment
Filename:
Alignment type :
codon (one-letter code)
amino acid
nucleotide
Code table :
Universal
Mitochondrial
Initial tree in newick format
None
From file:
Method
Amino Acid substitution model
Equilibrium frequencies:
equal to frequencies in sequences
equal to frequencies defined by the substitution model
Model:
HKY85(default)
JC69
K80
F81
F84
TN93
GTR
custom
Custom(6 digits string):
Addditional options:
Use an amino acid substitution model:
JTT
WAG
LG
KHGaa
mtREV
cpREV10
cpREV64
Variation over sites
None
Substitution rates
Discrete Gamma:
4 categories
8 categories
Initial values for alpha(shape parameter):
Default
Optimize α:
yes
no
Use Codon substitution model
Codon substitution model
Equilibrium frequencies:
equal to frequencies in sequences
equal to frequencies defined by the substitution model
Variation over sites
None
Substitution rates
Selective constraints
Discrete Gamma:
4 categories
8 categories
Initial values for alpha(shape parameter):
Default
Optimize α:
yes
no
Model for selective Constraints on amino acids:
EI (physico-chemical method)
JTT-ML91+ (estimated from JTT)
WAG-ML91+ (estimated from WAG)
LG-ML91+ (estimated from LG)
KHG-ML200 (estimated from KHG)
No amino acid dependence
ML parameters:
1 (w
0
; non-/synonymous rate ratio only)
5 (β, w
0
, σ, m, m
tc|ag
/ m
[tc][ag]
, m
ag
/ m
tc[ag]
)
8 (β, w
0
, σ, m, m
tc|ag
/ m
[tc][ag]
, m
ag
/ m
tc[ag]
, f
a
, f
c
, f
g
)
12 (β, w
0
, σ, m, m
tc|ag
/ m
[tc][ag]
, m
ag
/ m
tc[ag]
, m
ta
/ m
[tc][ag]
, m
tg
/ m
[tc][ag]
, m
ca
/ m
[tc][ag]
, f
a
, f
c
, f
g
)
1
4
7
11
12
Initial values for parameters:
Estimates for
nuclear genes
cpDNA
mtDNA
or
simple default values
as follows
Probability of neutral substitutions between amino acids a and b: approximated by exp(βw
ab
+ w
0
(1-δ
ab
))
β
Default
w
0
Default
Mutation rate variation of Gamma distribution can be assumed.
Scale parameter of the Gamma distribution (σ = 0 means no rate variation):
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]
(transition to transversion rate ratio):
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
(Note: The optimization should be done only if a simple substitution model is used.)