Question: Whole Genome Phylogeny
4
gravatar for Gorysko
7.9 years ago by
Gorysko100
Germany
Gorysko100 wrote:

Maybe You could advice some method for making whole genome phylogeny. Or it should be only whole genome alignment provided? In web I've found only this stuff http://ggdc.gbdp.org/ Maybe some one could say about advantages of it Thank you

genome phylogeny • 3.3k views
ADD COMMENTlink modified 6.3 years ago by Biostar ♦♦ 20 • written 7.9 years ago by Gorysko100

Are your looking within a population or between species?

ADD REPLYlink written 7.8 years ago by Zev.Kronenberg11k
1
gravatar for Josh Herr
7.9 years ago by
Josh Herr5.7k
University of Nebraska
Josh Herr5.7k wrote:

I've thought a little bit about your ideas on whole genome phylogeny before and I think it's computationally crazy.

Maybe you could tell us what you would like to discover by doing this? Are you just trying to understand the relationship of the organisms you study, in a taxonomic sense, or are you trying to understand how genome rearrangements are shaped by (or shape) the relationships of organisms. I guess I am not certain what your question is and how we can help you.

I know DNA-DNA hybridization has been used for a long time (since the early 70's I do believe) to understand species phylogenetics. Re-vamping these ideas, like the link you point out does, could be very interesting.

I think computationally the best we can do now is large suites of appropriately chosen marker regions (the emphasis here should be on phylogenetically informative sections of the genome which generally will be based on how broad a level of phylogenetics you are interested). You can do this using lots of programs such as PAUP, MrBayes, RAxML, etc., etc.

I think that looking at genome rearrangements can also be phylogenetically informative, and there are lots of ways to do this also. One of my favorite programs to use now for plants is SyMAP.

This is a huge area to investigate so feel free to give us more information on what your goals are. Good luck!

ADD COMMENTlink written 7.9 years ago by Josh Herr5.7k

all this is only identification of place in a world of one microorganism ( sorry I can't say the name of it). But the idea - to identificate ortholog genes, phylogeny of whole genome and of 16Srna etc

ADD REPLYlink written 7.9 years ago by Gorysko100

Whole genome phylogenies are more possible if you are dealing with smaller genomes than the euks. Check out this paper for a decent coverage of the topic: http://bioinformatics.oxfordjournals.org/content/21/10/2329.full

ADD REPLYlink written 7.9 years ago by Sulfolobus140
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