#       main topics:
UP      arb.hlp
UP      glossary.hlp
UP      arb_edit4.hlp
#       sub topics:
#SUB     subtopic.hlp
SUB     pt_server.hlp

# format described in ../help.readme


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.
