taxondna

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Produce a warning if the sum total of charsets is greater than that of the file

2

Specifically, was data dropped (charsets only cover 1-100 of a 300 bp file) or was data duplicated (charsets 1-300, 250-500 of a 500 bp file).

gaurav

Create character sets for 1, 2 and 3rd positions

3

We need to "hide" them in the output so we don't see them during import and complain of overlapping datasets. Possibilities: NEXUS: 1. Hide it in the "ASSUMPTIONS" block, whence...

gaurav

Alternatively, close Google Code issues display. Having two issue reporting sites might be confusing after launch.

gaurav

Cancelling a sequence in PD cancels the sequence next to it

1

This is odd, and should just be a mathematical oddity somewhere. Fixit!

gaurav

Some kind of checking to ensure data is being correctly manipulated

1

Possibilities: 1. Write another program to check the Nexus/TNT codon frequencies on the input file and output file. But this is an independent parser. 2. Set up a mode which...

gaurav

As of 668500a, we've got decent output messages on overlapped sequences. However, the error message is very confusing, with each exception in the chain adding more text to it. Let's...

gaurav

More or less works, but: 1. Exported datasets always come out as 'DNA'. 2. Check how symbolic exports work for TNT. 3. DNA ambiguity codes should be recoded as polymorphisms....

gaurav

When renaming taxa, the rows merge correctly, but a blank row remains for the defunct taxa

1

I wonder why.

gaurav

Unexcising a completely cancelled taxon leads to strange jumps in what is unexcised

1

Aha! A clue!

gaurav

Yeah.

gaurav