Is it possible to detect recombination from a core gene alignment? about clonalframeml

[xavierdidelot]

Hi Maria,

Yes the -xmfa_file true allows you to use a xmfa file as input which can contain multiple (unconcatenated) genes. R/theta is estimated for the whole set, not for each gene separately, but you could compute the number of recombination events that hit each gene from the list of all events contained in the output file with suffix importation_status.txt

Best wishes,
Xavier

[xavierdidelot]

Hello,

Yes you can use ClonalFrameML to analyse alignments of core genes. You need to prepare a xmfa file where each core gene sequence is a multi-fasta block separated by lines with just the '=' sign. So if you have each of your core genes as separate fasta files, you just need to add a '=' at the end of each file and concatenate these files to produce your xmfa input.

Best wishes,
Xavier

[rndg20]

Thank you so much for your reply. Just to clarify, I need to create separate multi-fasta files for each of the core genes (so 4059 multi-fasta blocks) and then concatenate them together with an '=' separating them.

As it stands my MSA is in the standard format (

Sample1
......
Sample2
.....)
and does not specify where genes start and end.

[xavierdidelot]

Yes, that's right. You will need to find out where genes start and end, because otherwise the software will assume that they occur next to each other which affects linkage and recombination detection.

[izabelcavassim]

One can only use the concatenation of genes under the xmfa format with the option "-xmfa_file true" included in the command. Right?

I am running it now, so am I going to get an estimate of R/theta for each gene? Is it unreliable to make an estimate per gene? Would you recommend LD based approaches instead?
Thank you!!

[izabelcavassim]

Thank you very much! Best, Maria Izabel

…

On Tue, May 5, 2020 at 4:55 PM Xavier Didelot ***@***.***> wrote: Hi Maria, Yes the -xmfa_file true allows you to use a xmfa file as input which can contain multiple (unconcatenated) genes. R/theta is estimated for the whole set, not for each gene separately, but you could compute the number of recombination events that hit each gene from the list of all events contained in the output file with suffix importation_status.txt Best wishes, Xavier — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#39 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB3WMCK5E66PJAMV2SKQ7BTRQASHDANCNFSM4CFVNX7Q> .

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