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15-taxon dataset processsing #6

Closed j-chou closed 9 years ago

j-chou commented 9 years ago

The 15-taxon dataset (caterpillar model species tree generated with MCcoal) (http://www.cs.utexas.edu/~phylo/datasets/binning-response/) has gene alignments in fasta format. We need to convert this to phylip format before running the other processing scripts. Ruth, I think you mentioned dendropy has this functionality?

redavids commented 9 years ago

Now I am not sure if Dendropy can handle gene alignments, maybe it just handles trees:

https://pythonhosted.org/DendroPy/tutorial/converting.html

Spend a few minutes searching the Dendropy library API. There is also this tool, which is what I'd look at first since I like python:

https://pypi.python.org/pypi/bioscripts.convert/0.4

And I just found this by googling:

http://sequenceconversion.bugaco.com/converter/biology/sequences/fasta_to_phylip.php

There must be zillion tools for this,

You should ask Nam or Siavash what they would use too. Or just google. Sorry! This is not something I've ever actually done so I just assumed Dendropy would convert alignments-maybe it does. I don't have time to search the API right now.

Best R

On Wed, Apr 22, 2015 at 1:39 PM, j-chou notifications@github.com wrote:

The 15-taxon dataset (caterpillar model species tree generated with MCcoal) (http://www.cs.utexas.edu/~phylo/datasets/binning-response/) has gene alignments in fasta format. We need to convert this to phylip format before running the other processing scripts. Ruth, I think you mentioned dendropy has this functionality?

— Reply to this email directly or view it on GitHub https://github.com/agupta0905/AGBsvdquartets/issues/6.

Ruth Davidson Department of Mathematics, University of Illinois Urbana-Champaign http://www.math.uiuc.edu/~redavid2/

j-chou commented 9 years ago

Ok, thanks Ruth! The one you linked to, Fast2Phylip.pl, works, so I'll try to get it done tomorrow.

syadu1988 commented 9 years ago

Hi Jed

Dendropy can handle Fasta data and it should just involve adding two lines to the taxon_relabeler.py script. Ashu or I have already made that change this morning so Ashu can discuss this with you after the class today. (I won’t be able to make it for the class today) and ask you to try it out.

Thanks Shashank

On Apr 23, 2015, at 7:08 AM, j-chou notifications@github.com wrote:

Ok, thanks Ruth! The one you linked to, Fast2Phylip.pl, works, so I'll try to get it done tomorrow.

— Reply to this email directly or view it on GitHub https://github.com/agupta0905/AGBsvdquartets/issues/6#issuecomment-95561882.