source: branches/properties/HELP_SOURCE/source/arb_pars_init.hlp

#Please insert up references in the next lines (line starts with keyword UP)
UP      arb.hlp
UP      glossary.hlp
UP      arb_pars.hlp
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#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.