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Last update on 04. Dec 2013 .
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Column statistic

OCCURRENCE

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
                +2 half mutations
                eg .'7' half number of mutations than '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.

 

BUGS

No bugs known