source: branches/tree/HELP_SOURCE/source/ne_align_seq.hlp

#Please insert up references in the next lines (line starts with keyword UP)
UP      arb.hlp
UP      glossary.hlp
UP      arb_edit4.hlp
#Please insert subtopic references  (line starts with keyword SUB)
#SUB    subtopic.hlp
SUB     pt_server.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           Old aligner from ARB_EDIT

OCCURRENCE      ARB_EDIT4/Edit/Old aligner from ARB_EDIT

DESCRIPTION     Aligns or realigns selected sequence with the database
                sequences. The most similar database sequences are
                found, and the new sequence is aligned with these according to
                primary and secondary structure similarity.

                Select whether to align the sequence of the selected species or
                all marked species.

                Select whether to align versus an explicit reference or
                the nearest relative reported by the PT_SERVER.

                The used relatives may be marked by checking 'Mark sequences
                found by the pt_server'.

                Press <GO>

NOTES           Marking the closest relatives allows manual optimization of the alignment
                of the new species with its closest relatives.

EXAMPLES        None

WARNINGS        The aligner version available with the present package often
                does not properly align short partial sequences.

BUGS            The aligner needs lots of computer memory, sometimes more than
                you have. In this case it may not align some sequences.

                The aligner does not align the last 3-6 bases of short sequences
                correctly. Look at the end of your sequences.