How to prep an input (nexus) file for BEAST/BEAUTi?

Question

[hallishtw]

I am working with bacterial whole genome sequences. I understand I have to do a multiple alignment (for which I used parsnp on my de novo assembled genomes) and remove recombination first. I detected the recombination sites with Gubbins but did not get an output of multiple alignment where the recombination sites are removed. So now I am unsure as to how to proceed. I assume I have to somehow remove this recombination sites and convert the alignment to a nexus file for BEAUTi. Alternative ways to proceed are also appreciated. Thanks in advance!

[sridhar56]

I am not sure if you have to remove the recombination. Isnt the recombination information useful to help you identify evolution and understand the phylodynamics?

I have created a Multiple Sequence Alignment file and then done the analysis in the past.

[hallishtw]

Hi thanks for your comment.That was also my first assumption as well. But after looking into literature, it seems like recombination is "noise" in the process. Even if you skipped the recombination filtering process, how would you convert the .xmfa (parsnp output) or converted .maf file to nexus for BEAUTi? Multiple sequence alignment of sequenecs of different length