Tutorial data

[Leonardo Borges]

Does anybody has the sample files used in the POY 4.0 tutorial?

The referred ftp address to download it (  ftp://ftp.amnh. org/pub/group/molecular/poy/POY4/docs/data/SampleData.zip. ) does not exist.

Thanks!

Leonardo

[Nicholas Lucaroni]

That will be one of the first links on the following page,
http://www.amnh.org/our-research/computational-sciences/research/projects/systematic-biology/poy/sample-files-data-sets

[Leonardo Borges]

Thanks Nicholas, but I have seen this page and the files are not the same.

Or at least they do not have the same names.

Leonardo

[Nicholas Lucaroni]

Gotcha, if you've pulled that ftp link from the POY 4.0 Tutorials: general commands [1] document then SOME of those files can be found in the code repository [2] with minor name changes. I couldn't find 1Fitch.ss on an older machine we have here, but I would imagine that can be replaced with 30.ss from the repo. All those data-sets have the same taxa names (except for 2.fas), so they can be combined in any way you'd like. Some have partitions, some can be read as prealigned (listed in align_fas and align_aa), et cetera. Sorry for the inconvenience.

nick

[1] - http://www.amnh.org/content/download/56593/889428/file/general_commands.pdf
[2] - https://code.google.com/p/poy4/source/browse/#hg%2Ftest

[Leonardo Borges]

That's exactly it, Nicholas.

Guess that even with the changes I will be able to follow up the tutorial ;)

Thanks,

Leonardo

[Leonardo Borges]

Nick,

I have been able to follow the tutorial without problems, but now I am stuck by the lack of a file "course.fasta".

Could not find it in the source code page.

Do you happen to have it?

Thanks,

Leonardo