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xavierdidelot / ClonalFrameML

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
GNU General Public License v3.0
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Is it better to order genes by the reference genome for a xmfa file ??? #135

Closed yayahoho1 closed 2 years ago

yayahoho1 commented 2 years ago

Hi, Xavier I know that it would be better to use a fasta file as input instead of a xmfa file. But i only have core gene alignment, would it better to order the genes by a reference? Does it work for ClonalFrameML?

Thanks in advance!

Kind regards, YiLin

xavierdidelot commented 2 years ago

Hi YiLin,

When using a xmfa file as input, the order of the genes should not have much effect on the recombination results. So you could order them as in the reference, especially if it makes it easier for you to interpret the output.

Best wishes, Xavier

yayahoho1 commented 2 years ago

Thank you Xavier!