Is it better to order genes by the reference genome for a xmfa file ???

[yayahoho1]

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]

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]

Thank you Xavier!