Question: Phylogenomic tree construction
0
gravatar for manjumoorthy95
3 months ago by
manjumoorthy9510 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 • 142 views
ADD COMMENTlink modified 3 months ago by piet1.7k • written 3 months ago by manjumoorthy9510

You can use phylogeny.fr

ADD REPLYlink written 3 months ago by jaqx00850

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

ADD REPLYlink written 3 months ago by manjumoorthy9510

How much is the largest of the genomes?

ADD REPLYlink written 3 months ago by jaqx00850

each strain has around 4.9 mb as the genome size.

ADD REPLYlink written 3 months ago by manjumoorthy9510
2
gravatar for piet
3 months ago by
piet1.7k
planet earth
piet1.7k 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 3 months ago • written 3 months ago by piet1.7k

ok I will try that way

ADD REPLYlink written 3 months ago by manjumoorthy9510
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1655 users visited in the last hour