TODO

                       TODO for Clearcut

                    Version 1.0.4 -- Nov 2004

                         Luke Sheneman
                     sheneman@cs.uidaho.edu
                           11/15/04

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SHORT TERM:
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1) Add flag to allow matrix output in different formats (upper/lower)

2) Add bootstrapping functionality

3) Retroactively comment code further (in progress)

4) Fix problem where 2nd taxon in dmat can't start with +,-,.

5) Add regression test suite



LONG TERM:
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1) Combine distance matrix and multiple alignment parser into a
   single state machine.  This would allow clearcut to autodetect
   the type of input and the user would not have to specify.

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