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Last update on 06. Sep 2018 .
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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 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.

     

    BUGS

    No bugs known