Unclear how XMFA should be formatted

[GoogleCodeExporter]

It appears that CFML does not accept XMFA as formatted by Mauve. It is unclear 
how this file should be formatted.

What steps will reproduce the problem?
1. Using standard Mauve-formatted XMFA, I get the error message:
ERROR: readXMFA(): File ../CC11_SGW_Complete.xmfa did not begin with '>'

2. I can strip out the comment lines (#), but that removes the sample naming 
key (i.e. samples are named 1,2,3 ... which is not what I used in my guide tree)

How are XMFA files supposed to be formatted? Will it work if we use the 
"seqnum" identifiers for the guide tree? Or conversely, could we replace the 
"seqnum" identifiers in the XMFA with the sample names?

Thanks.



Please provide any additional information below.

Original issue reported on code.google.com by acretchl...@gmail.com on 29 May 2015 at 4:12

[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 xavier.d...@gmail.com on 2 Jun 2015 at 10:06

• Changed state: Done