Google
More docs on the ARB website.
See also index of helppages.
Last update on 04. Dec 2013 .
Main topics:
Related topics:

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 start-up 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 start-up time. Sequence changes afterwards are ignored. Restart arb_parsimony if you want them to take effect.