This question is probably for Aaron. Thank-you Aaron for all your hard
work on this software and the others.
We are aligning 16 (or more) bacterial genomes to update some species
classifications. The problem is a lot of horizontal gene transfer in
these bugs. After a 16 genome alignment, and using MCM, A phylogenetic
tree would be a nice start. Accordning to the MAUVE manual: "Note that
the guide tree is not intended to be a phylogeny indicative of the
genealogy of input genomes. It is merely a computational crutch for
progressive genome alignment. Also note that alignments are later
refined independently of a single guide tree toplogy to avoid biasing
later phylogenetic inference." I've seen many questions related to
phylogeny, and have seen redirections to the Clonal Frame and Clonal
Origin software at this link:
https://code.google.com/p/clonalorigin/wiki/FromGenomeAssemblyToRecombination
I would like to do a phylogenetic analysis, but really like the
recombination analysis found at the above link. So how to do both?
First, there are simple biologist-type questions:
1. Clonal Frame and Clonal Origin are not going to give me a phylogeny
"indicative of the genealogy" are they? What is the Newick tree
generated by "getClonalTree core_clonalframe.out.1 clonaltree.nwk" based
on? The answer is "clonal genealogy" (I suspect) but reading the
manuscript by Didelot (2010) was relatively difficult for my background
and left me wanting a simple description.
2. After getting "a fully resolved consensus tree" and wanting to move
on with ClonalOrigin, a dumb question I have to ask is "Where do I find
the number of alignment blocks to use in the "Run ClonalOrigin on each
alignment block" steps?
Some technical questions are:
1. Do ClonalFrame or ClonalOrigin use MPI, or am I wasting cores
requesting more than one per job? ClonalFrame took 20 days to complete
on our new cluster. Should I request a fat node (250 Gb RAM)?
2. When I get to the "Run ClonalOrigin on each alignment block" step, is
this multithreaded?
3. Same question for "Run ClonalOrigin with global parameters".
That's enough for now. Thanks again.
-peter
--
-
Peter R. Hoyt, Ph. D.
Graduate Program Director, Bioinformatics Certification
Oklahoma State University
Department of Biochemistry and Molecular Biology
110FB Henry Bellmon Research Center
(Shipping address: 246 Noble Research Center)
Stillwater, OK 74078
(405) 744-6206
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