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#Please insert up references in the next lines (line starts with keyword UP)
UP arb.hlp
UP glossary.hlp
UP arb_pars.hlp
#Please insert subtopic references (line starts with keyword SUB)
#SUB subtopic.hlp
# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
#************* Title of helpfile !! and start of real helpfile ********
TITLE 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.
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