source: branches/stable/HELP_SOURCE/oldhelp/user_matrix.hlp

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UP      glossary.hlp

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#************* Title of helpfile !! and start of real helpfile ********

TITLE           User Defined Distance Matrix

OCCURRENCE      ARB_DIST

DESCRIPTION     Allows the user to define distances between different bases.
                E.g. An A-T should get a smaller difference
                as an A-G, so the corresponding matrix elements should be set
                to 1.0 and 2.0.

NOTE            Before the algorithm starts, all matrix values will be 
                multiplied by a factor, such that the average matrix value
                (except the diagonal) is approximately 1.0!

                To save a user matrix use <Properties/Save Properties> menu
                item.

BUGS            Works only with some distance corrections:

                        none    similarity      jukes_cantor

                Works only with dna

                If enabled only ACGTU/GAPS bases are calculated.