Calculates the base and frequencies positional variability for each column independently.
It uses the parsimony method to find the minimum number of mutations for each site, as they are determined by the specified topology.
The calculation is performed for sequences of all species in tree. For best results you should use one of the biggest trees available. The tree should have been optimized using ARB_PARSIMONY.
The result can be used by:
Parsimony to weight the characters properly
Neighbour joining to estimate the distances more accurately.
Filter (read notes below)
Resulting SAI will contain the following character codes:
'.' Less than 10% valid characters
'-' No mutations.
'0123456789ABCDE...' Mutation rate category
The higher the digit/character of the mutation rate category is, the more conserved the site is. Stepping 2 positions rightwards in the list of given characters, approximately halves the mutation rate (explicit mappings see below).
Valid characters are "ACGTUacgtu" for DNA/RNA (or all amino acid codes for AA sequences).