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
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):
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
for nuclear genes, for cpDNA, for mtDNA or as follows: initial values of nucleotide exchangeabilities [m_ij]: ratio (m) of double/triple to single/double nucleotide changes: _0.0__ m_tc|ag /m_[tc][ag]: _1.0__ m_ag / m_tc[ag]: _1.0__ m_ta / m_[tc][ag]: _1.0__ m_tg / m_[tc][ag]: _1.0__ m_ca / m_[tc][ag]: _1.0__ initial values of nucleotide equilibrium frequencies [f_i]: f_a: 0.25 f_c: 0.25 f_g: 0.25
Optimize tree
yes
no