Unclear how XMFA should be formatted about clonalframeml

[GoogleCodeExporter]

Hi Adam,

Indeed CFML will not accept XMFA produced by Mauve, but it should not be too 
much work to reformat. You should remove comment lines, and keep on the header 
lines only the strain names preceded by the > symbol. So since Mauve uses 
indexes, you could keep for example only '>1' in the first line, etc. It does 
mean though that you will need the starting tree to use the same names. Or if 
you want to keep you tree file as it is, you will have to replace indexes with 
full names in the xmfa file. Either way, the xmfa and tree files need to use 
exactly the same strain names.

Best wishes,
Xavier

Original comment by [email protected] on 2 Jun 2015 at 10:06

• Changed state: Done