Question: Phylogenomic tree construction
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gravatar for manjumoorthy95
14 months ago by
manjumoorthy9520 wrote:

I wanted to construct phylogenomic tree using the whole genome of certain bacterial strains. can anybody help me with suggestions of softwares or webservers to use?

phylogenomics • 378 views
ADD COMMENTlink modified 14 months ago by piet1.8k • written 14 months ago by manjumoorthy9520

You can use phylogeny.fr

ADD REPLYlink written 14 months ago by jaqx00870

But i wanted to use the entire genome of 15 strains of bacteria.

ADD REPLYlink written 14 months ago by manjumoorthy9520

How much is the largest of the genomes?

ADD REPLYlink written 14 months ago by jaqx00870

each strain has around 4.9 mb as the genome size.

ADD REPLYlink written 14 months ago by manjumoorthy9520
2
gravatar for piet
14 months ago by
piet1.8k
planet earth
piet1.8k wrote:

construct phylogenomic tree using the whole genome of certain bacterial strains

I would advise not to use whole genomes for phylogeny. You should restrict your analysis to highly conserved genes from the core genome and you should exclude repeats and sites which presumably have arisen by any kind of recombination (mobil elements, transposons, tandem repeats, prophages ...). Recombination breaks clonality.

ADD COMMENTlink modified 14 months ago • written 14 months ago by piet1.8k

ok I will try that way

ADD REPLYlink written 14 months ago by manjumoorthy9520
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