Question: xmfa format? about clonalframeml

[xavierdidelot]

Yes, ClonaFrameML ignores everything after the colon in the fasta headers.

[nbawe]

PS! I have edited my original question!

[xavierdidelot]

The lines starting with # are comments and should not have any effect.

[nbawe]

Thank you!

[nbawe]

@xavierdidelot one more question. I have tree file with names like: >22275|OXC7093 but xmfa has names like: >22275|OXC7093:1-1323 + CAMP0001. I ran CFML using the mentioned files and it finished without any errors. The CFML output has names like in the tree file 22275|OXC7093.

My question is how does CFML handles the differences in the names? Does it exclude everything after colon (including colon sign)?

Thank you for the answer

[nbawe]

I wanted to clarify where the difference comes from. I am using pubMLST database, where I got concatenated core fasta from which I build tree with RAxML. RAxML generated tree is used in combination with pubMLST database core xmfa using CFML. So the names differ as mentioned in previous comment.

[nbawe]

Thank you!