Tools for Phylogenetic Trees

[ElMichael]

Hi,
I'm rather far from the field of computational phylogenetics, so sorry for basic questions.
I have several tens of bacterial species in my sample (just the names, not sequences) and what I want is to build something like tree or cladogram to understand how close they are to each other based on the similarity of their known whole genome sequences.
I mean some tools where I can enter, e.g., gi numbers for the genome sequences of the bacteria of interest, and get a cladogram as output.
Any other advice how to identify and vizualize relationship between number of bacteria would be appreciated (apart from the direct pairwise comparison by BLAST).
Thanks!

[fanyucai1]

MEGAN is a versatile tool for analyzing taxonomic and functional content of metagenomes. It allows comparative analyses of different datasets.

[cliffbeall]

I think it would be hard to use the whole genomes because it diverges so much once you get above genus level.

There is a paper by Wu and Eisen where they make trees for bacteria using an alignment of 31 housekeeping genes. You might want to look at their methods.

1: Wu M, Eisen JA. A simple, fast, and accurate method of phylogenomic inference.
Genome Biol. 2008 Oct 13;9(10):R151. PubMed PMID: 18851752; PubMed Central PMCID:
PMC2760878.

[ElMichael]

fanyucai1, cliffbeall, thanks for advice!

[colindaven]

There is a taxonomic program called Jspecies available which attempts to compare species on the basis of whole genome data. I haven't tried it yet though but it looks very capable.