TaxonDNA release: 0.9.3

[Gaurav Vaidya]

Hi everybody,

TaxonDNA gets bumped up a notch, both because it feels
a lot more stable than usual (no strange glitches, no
weird stuff that it doesn't recover from, etc.),
atleast on my comp and my sample datasets. As usual,
you can download it from the TaxonDNA Sourceforge
project page, or get it by following this link
[http://sourceforge.net/project/showfiles.php?group_id=145950&package_id=160630&release_id=419480]

There's a couple of bug fixes (Guanyang will be happy
that the no-allo matches are being counted, and will
be disappointed that the Species Summary still isn't
as descriptive as it was pre-0.9), but it's mostly new
features, which means that there are likely to be more
bugs in 0.9.3 :). Fun for the whole family.

The new features include:
1. The Exporter: Allows you to export your file in a
number of ways by picking options. There is also a
split-this-file-into-multiple-small-files options -
use with care, it will spew files into whichever
directory you point it!
2. Complete Overlap: This will walk along the
sequence, and determine which area of the sequence has
the maximum number of overlap. It is also possible to
extract this region as a FASTA file.

Sorry if this e-mail is a little weird, I'm a bit
dazed right now :). Please report any bugs you see
either to me, to this mailing list, or to the
Sourceforge project page bug list
[http://sourceforge.net/tracker/?group_id=145950&atid=763567]

cheers,
Gaurav

---
Another day, another destiny.

[Zhang Guanyang]

Please notice the changes. > needs to be leading a taxon name

and it isn't necessary to put [1539] after every taxa (seq).

#NEXUS
BEGIN DATA;
DIMENSIONS NTAX=458 NCHAR=1539;
FORMAT DATATYPE=DNA MISSING=. GAP=- ;
MATRIX
>Acanthocnema_glaucescens ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTAATTTTAGCAGGATTTGGTATACTCTCACATATTATTAGCCAAGAATCAGGAAAAAAAGAAACATTCGGTTCTTTAAGAATAATTTATGCAATATTAGCAATTGGTTTATTAGGATTTATTGTTTGAGCTCATCATATATTTACTGTAGGTATAGATGTAGATACACGAGCATATTTTACTTCAGCAACAATAATTATTGCTGTACCTACAGGTATTAAAATTTTTAGTTGATTAGCTACTTTATACGGAACTCAATTAAATTATTCACCTGCTACTTTATGAGCTTTAGGATTTGTTTTTTTATTTACTGTAGGAGGATTAACTGGAGTAGTATTAGCAAATTCTTCAGTAGATATTATTTTACATGATACTTATTATGTAGTAGCTCATTTTCACTATGTACTATCAATAGGAGCCGTATTTGCTATTATAGCAGGATTTGTACATTGATATCCATTATTTACTGGATTAACAATAAACAATACTTTATTAAAAAGTCAATTTATTATTATATTTATTGGAGTAAATTTAACATTTTTTCCTCAACATTTTTTAGGTTTAGCTGGTATACCTCGACGATATTCAGACTATCCAGATGCTTATACTACATGAAATGTAGTTTCAACTATCGGATCAACAATTTCATTATTAGGAATTTTATTTTTCTTTTTTATTATTTGAGAAAGTTTAATTTCACAACGACAAGTATTATTCCCAATTCAATTAAATTCTTCAATTGAATGATCACAAAATACTCCACCAGCTGAACATAGTTATTCTGAATTACCTTTATTAACTAATTTC

>Acerocnema_macrocera ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTAATTTTACCTGGATTTGGTATAATTTCTCATATTATCAGCCAAGAATCAGGAAAAAAGGAAACTTTTGGTTCATTAGGAATAATTTATGCTATATTAGCTATTGGTTTATTAGGATTTATTGTATGAGCTCATCATATATTTACTGTAGGTATAGATGTTGATACACGAGCATATTTTACTTCAGCAACAATAATTATTGCTATTCCAACTGGAATTAAAATTTTTAGATGATTAGCTACTTTATACGGAACTCAATTAAATTATTCCCCAGCTACTCTGTGATCTTTAGGATTTGTTTTTCTATTTACTGTAGGAGGATTAACAGGAGTTGTTTTAGCAAACTCATCAGTAGATATCATTTTACATGATACTTATTATGTAGTAGCTCATTTTCATTATGTACTATCAATGGGAGCCGTATTTGCTATTATAGCAGGATTCGTTCATTGATACCCATTATTCACTGGATTAACAATAAATAATACTTTATTAAAAAGACAATTTATTATTATATTCATTGGAGTAAATTTAACATTTTTCCCTCAACATTTTTTAGGACTAGCAGGAATACCACGACGATATTCAGATTATCCAGATGCTTATACAACATGAAATGTAATTTCAACTATTGGATCAACAATTTCATTACTTGGAATTTTATTTCTATTTTTTATTATTTGAGAAAGTTTAATTTCTCAACGTCAAGTATTATTTCCTATTCAATTAAATTCTTCAATTGAATGATTACAAAATACTCCCCCAGCTGAACACAGCTATTCTGAATTACCTTTATTAACTAATTTC

;
END;

OLD ONE:

#NEXUS
BEGIN DATA;
DIMENSIONS NTAX= NCHAR=600;
FORMAT DATATYPE=DNA MISSING=. GAP=- ;
MATRIX
Acanthocnema_glaucescens ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTAATTTTAGCAGGATTTGGTATACTCTCACATATTATTAGCCAAGAATCAGGAAAAAAAGAAACATTCGGTTCTTTAAGAATAATTTATGCAATATTAGCAATTGGTTTATTAGGATTTATTGTTTGAGCTCATCATATATTTACTGTAGGTATAGATGTAGATACACGAGCATATTTTACTTCAGCAACAATAATTATTGCTGTACCTACAGGTATTAAAATTTTTAGTTGATTAGCTACTTTATACGGAACTCAATTAAATTATTCACCTGCTACTTTATGAGCTTTAGGATTTGTTTTTTTATTTACTGTAGGAGGATTAACTGGAGTAGTATTAGCAAATTCTTCAGTAGATATTATTTTACATGATACTTATTATGTAGTAGCTCATTTTCACTATGTACTATCAATAGGAGCCGTATTTGCTATTATAGCAGGATTTGTACATTGATATCCATTATTTACTGGATTAACAATAAACAATACTTTATTAAAAAGTCAATTTATTATTATATTTATTGGAGTAAATTTAACATTTTTTCCTCAACATTTTTTAGGTTTAGCTGGTATACCTCGACGATATTCAGACTATCCAGATGCTTATACTACATGAAATGTAGTTTCAACTATCGGATCAACAATTTCATTATTAGGAATTTTATTTTTCTTTTTTATTATTTGAGAAAGTTTAATTTCACAACGACAAGTATTATTCCCAATTCAATTAAATTCTTCAATTGAATGATCACAAAATACTCCACCAGCTGAACATAGTTATTCTGAATTACCTTTATTAACTAATTTC [1539]

Acerocnema_macrocera ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTAATTTTACCTGGATTTGGTATAATTTCTCATATTATCAGCCAAGAATCAGGAAAAAAGGAAACTTTTGGTTCATTAGGAATAATTTATGCTATATTAGCTATTGGTTTATTAGGATTTATTGTATGAGCTCATCATATATTTACTGTAGGTATAGATGTTGATACACGAGCATATTTTACTTCAGCAACAATAATTATTGCTATTCCAACTGGAATTAAAATTTTTAGATGATTAGCTACTTTATACGGAACTCAATTAAATTATTCCCCAGCTACTCTGTGATCTTTAGGATTTGTTTTTCTATTTACTGTAGGAGGATTAACAGGAGTTGTTTTAGCAAACTCATCAGTAGATATCATTTTACATGATACTTATTATGTAGTAGCTCATTTTCATTATGTACTATCAATGGGAGCCGTATTTGCTATTATAGCAGGATTCGTTCATTGATACCCATTATTCACTGGATTAACAATAAATAATACTTTATTAAAAAGACAATTTATTATTATATTCATTGGAGTAAATTTAACATTTTTCCCTCAACATTTTTTAGGACTAGCAGGAATACCACGACGATATTCAGATTATCCAGATGCTTATACAACATGAAATGTAATTTCAACTATTGGATCAACAATTTCATTACTTGGAATTTTATTTCTATTTTTTATTATTTGAGAAAGTTTAATTTCTCAACGTCAAGTATTATTTCCTATTCAATTAAATTCTTCAATTGAATGATTACAAAATACTCCCCCAGCTGAACACAGCTATTCTGAATTACCTTTATTAACTAATTTC [1539]

;
END;