Phylogenomic tree construction

Question

[manjumoorthy95]

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?

[jaqx008]

You can use phylogeny.fr

[manjumoorthy95]

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

[jaqx008]

How much is the largest of the genomes?

[manjumoorthy95]

each strain has around 4.9 mb as the genome size.

Answer 1

[piet]

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.

[manjumoorthy95]

ok I will try that way