#       main topics:
UP      arb.hlp
UP      glossary.hlp
UP      arb_pars.hlp
#       sub topics:
#SUB     subtopic.hlp

# format described in ../help.readme


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.
