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More documentation can be found on the ARB website.
Last update on 08. Apr 2009 .
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ARB PARSIMONY INTRO ( Filter Weights )

OCCURRENCE

ARB_NT/Tree/Add Species to Tree

 

DESCRIPTION

Set basic options for the parsimony program. If you do not want to use a filter, you should select a filter (eg. E. coli) which excludes only the big gaps in the alignment. Otherwise the program will count thousands of uninformative columns. If you want a transversion parsimony, open the filter window, and change the "simplify" option to TRANSVERSIONS ONLY

 

NOTES

After pressing go, no species is added, no tree is changed, you only get a new window (with some action buttons).

 

WARNINGS

You can only change filter settings at startup time. You should use filters in combination with large databases to speed up computation. Gaps ('-') are treated as bases, so check for gaps at the beginning or end of short sequences. Replace them by '.'.

 

BUGS

All sequences are read at startup time. Sequence changes afterwards are ignored. Restart arb_parsimony if you want them to take effect.