| More docs on the ARB website. See also index of helppages. Last update on 27. Jun 2017 .

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.