Phylogeny using whole proteomes

[standonn]

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

[colindaven]

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/

[standonn]

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!

[Richard Finney]

Check out the "ape" package available in R.
You can save the tree in newick format.

[standonn]

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.