Question: Whole Genome Tree
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gravatar for amresharma1
3 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 3 months ago by Mensur Dlakic2.4k • written 3 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 3 months ago by Joe15k
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gravatar for Mensur Dlakic
3 months ago by
Mensur Dlakic2.4k
USA
Mensur Dlakic2.4k 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 3 months ago by Mensur Dlakic2.4k
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gravatar for Carambakaracho
3 months ago by
Carambakaracho1.9k
Switzerland/Basel
Carambakaracho1.9k wrote:
ADD COMMENTlink modified 3 months ago • written 3 months ago by Carambakaracho1.9k
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