Question: Whole Genome Tree
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gravatar for amresharma1
12 months ago by
amresharma10 wrote:

I had 50-60 bacterial strains of length 1.5Mb (bp average). I want to construct genome tree by doing multiple genome alignment. Please provide me with guidlines/tools.

ADD COMMENTlink modified 12 months ago by Mensur Dlakic6.5k • written 12 months ago by amresharma10
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It's functionally impossible to multiply-align whole genomes.

You need to explore using mash distances, or create clustered, concatenated orthologue alignments.

ADD REPLYlink written 12 months ago by Joe18k
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gravatar for Mensur Dlakic
12 months ago by
Mensur Dlakic6.5k
USA
Mensur Dlakic6.5k wrote:

I get it that there are reasons for whole genome alignments, but making genome trees does not strike me as one of them. Unless all your strains are very related to each other and you are trying to tease out subtle differences, I doubt you will gain much useful information from this exercise.

Instead, there is a tool called ezTree that will look at multiple genomes, predict their ORFs, find single-copy marker genes they all share, and build a tree from their concatenated alignments. The last step can certainly be done better - I do it manually outside of this pipeline - but I think this general approach is more likely to give you useful information.

ADD COMMENTlink written 12 months ago by Mensur Dlakic6.5k
0
gravatar for Carambakaracho
12 months ago by
Carambakaracho2.2k
Germany/Cologne
Carambakaracho2.2k wrote:
ADD COMMENTlink modified 12 months ago • written 12 months ago by Carambakaracho2.2k
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