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Alignment

Filename:

Alignment type

Code table

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Method

This text will never shown. Standard method menu part will be inserted here with javascript.

This text will never shown. Another Standard menu will be inserted here with javascript. In case Alignment type=amino acid (for the "Codon substitution model" part).

Selective Constraints on Amino Acids:

ML parameters:

Initial values for parameters:
  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

Amino Acid substitution model
Equilibrium frequencies:
Variation oversites
Discrete Gamma:
Initial values for alpha(shape parameter):
To be Optimized:
Options:
Amino Acid exchangeabilities:
Codon substitution model