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Main topics: ARB: a Short Introduction Glossary ARB Parsimony | Related topics:
# ARB PARSIMONY INTRO ( Filter Weights ) OCCURRENCE DESCRIPTION NOTES WARNINGS BUGS ## 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.