I have used JML for mito-nuclear discordance in a group of earthworms, and I think it worked well. It was not to hard to set up the analysis, and it was quite easy to interpret the output.

Could you explain please how should I prepare input files if I have three nuclear markers with concordant topology and one mytochondrial with diferent topology. Am I right if I make xml file with tree nuclear and *.phy file with mitochondrial. May be you know an article where I can find detailed description of input file preparation?

It is quite well described in the manual, you need three input files. A treefile from a *beast analysis, a phy file with sequences from the marker you want to test, and finally a control file, stating the number of species, number of sequences for each species, the evolutionary rate for the marker, the ploidy level, or heredity scalar, and other things, I add one I used in my analysis.

The sequences in the phy file shoud be named using the same species name given in the control file followed by a number.

Hope this helps!

I have not used the software for some time, so I may have forgotten something

Hi there, sorry to bother you again on this topic.

It is still not clear to me whether the xml file and the *.phy files should be made based on different markers (i.e. the xml with the nuclear and the phy with the mitochondrial data in the case reported by Bodrov Semyon), or they should be both referring to a single dataset (thus repeating twice the analyses)