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Old 03-11-2016, 01:36 AM   #1
standonn
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Default Phylogeny using whole proteomes

Dear all,

I have the proteome (and genome) of several species of nematodes. I would like to build the phylogeny of these species. Ultimately I would like a newick tree (which I could use as an input for CAFE)

Do you know how to build phylogenies from whole proteomes/genomes?

Best,
Sophie
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Old 03-11-2016, 03:06 AM   #2
colindaven
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It won't get you to a newick file or standard output format at present, and requires a shell script and a bit of work, but MASH is a fast and fascinating approach.

You can use you genomes with it (not proteomes as far as I know), but read the cautionary note in the preprint too.

http://mash.readthedocs.org/en/latest/
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Old 03-11-2016, 04:51 AM   #3
standonn
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Thanks for your answer! Mash seems like a very interesting tool indeed! I wonder if it wouldn't be possible to get a newick tree from it...
I'll be studying it!
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Old 03-11-2016, 05:23 AM   #4
Richard Finney
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Check out the "ape" package available in R.
You can save the tree in newick format.
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Old 03-14-2016, 04:34 AM   #5
standonn
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Thank you for your answer!
I actually was able to run Mash and then input the distance matrix into ape to build a phylogenetic tree (and get it in Newick format)! It worked very good and the analysis was done very fast.
Ape is a very nice package. Thanks for pointing it out to me.
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