Phylogeny using whole proteomes

standonn · 03-11-2016, 02:36 AM

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 · 03-11-2016, 04:06 AM

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 · 03-11-2016, 05:51 AM

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 · 03-11-2016, 06:23 AM

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

standonn · 03-14-2016, 05:34 AM

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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03-11-2016, 02:36 AM	#1
standonn Member Location: UK Join Date: Nov 2014 Posts: 14	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

03-11-2016, 04:06 AM	#2
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	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/

03-11-2016, 05:51 AM	#3
standonn Member Location: UK Join Date: Nov 2014 Posts: 14	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!

03-11-2016, 06:23 AM	#4
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	Check out the "ape" package available in R. You can save the tree in newick format.

03-14-2016, 05:34 AM	#5
standonn Member Location: UK Join Date: Nov 2014 Posts: 14	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.