I'm doing NGS and I published a whole genome of Pseudomonas aeruginosa bacteria. I want to construct a phylogeny based on whole genome not with either 16s or housekeeping genes.
Is there any online tool available for this or windows based software for the same?
Genome based phylogenetic trees is not widespread because of very hard processing of so large massives of information. In addition different parts of genome has different rates of evolution changes. For constructing full genome phylogenetic trees you must have genomes of all organisms you want include in your analysis. Also please note that you must have powerful computers to do this, because genomes are very large and hard to compare. You can try to do this by using some Linux based software. Also you may use more easy way - to use parts of genomes for constructing number of different phylogenetic trees. On the basis of this you can make consensus tree. But all depends on your aims.
Best wishes
I would be very hesitant about constructing a phylogeny using a whole genome sequence, especially of a pathogen like P. aeruginosa. These species often have very high rates of horizontal transfer, and of some very large pieces of DNA. Further, translocations or inversions are quite common. And unless you're using an evolutionary model that accounts for these sorts of things, the phylogeny you get out could be very misleading. I'm not aware of a model that could account for this, but assuming you had one I think you'd have to use some sort of ML or Bayesian analysis to accommodate the complexity. And I doubt any of the well-used tools would finish in a reasonable time frame.
I would advise that a better idea would be to gather up several stable genes from each genome, and simply concatenate them together. You could then perform a phylogenetic analysis on long sequences. Again, not a methodology without its downsides, but it is commonly done, and should give you a better picture of the phylogenetic history than whole-genome alignment.
I am extremely thankful to Dr. Andrii, Dr, Arthur and Dr. David for your input which enlight me to right direction.
As per my experience also, i never found a phylogeny with whole genome, and all papers denoting to a certain genes and or blocks, hence i thought to do it as a whole its possible for the computational strength is a questionable one.
I understood from the above answers individual gene trees is the best option for my bacterial interest as its highly evolving bacteria.
Thanks all once again for your precious time spent for my query.
There is an option but the interpretation is up to you...
http://tlife.fudan.edu.cn/cvtree/
There is a lots of tool for genome phylogeny i would suggest you a few of them,
NDTree, MEGAX, CSI Phylogeny and REALPHY. go ahead
You can use best option MEGA-X or any other software but only thing you required is heavy computer with heavy processors and high RAM.
Naveen Chaudhary Could you please suggest a clear workflow for using MEGAx, since I could not find a mention for WGS uploading data?
Murugan Nandagopal thanks for this question! could you please re-answer your question in 2021 based on the experience you may got !
Mohannad Mahmoud
The same problem is here in this question too as it was in previous question you found regarding this topic. People tend to suggest tool to do certain thing but they did not understand the concept or read the question well. Nevertheless, this question was asked in 2014 and several of the tools and processors available today were not present at that time. However, the explanation from David Michael Curran is still relevant. So, please make a workflow for processing your data followed by phylogenetic analysis.
please use this website (https://tygs.dsmz.de./) to draw Phylogenetic tree using whole genome sequence , just put genome accession numbers and get your tree. if you have more than 20 genomes you can send email ( [email protected] ) for upgrade your genomes numbers.
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