ARB_NT/SAI/Create SAI from Sequences/Positional Variability ...
DESCRIPTION
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.
The result can be used by:
Parsimony to weight the characters properly
Neighbour joining to estimate the distances more accurately.
Filter
Result:
'.' Less than 10% valid characters
'0123456789ABCDE...' The higher the number the more conserved the site is.
Stepping 2 position rightwards in the list of given char,
means half number of mutations (eg .'7' means "half number
of mutations compared to '5'")
NOTES
Use the biggest tree you have.
NOTES
@@@ Compare it to consensus and max frequency.
WARNINGS
if you have only small trees (<100 species), forget this function.