BEAST analysis with multiple loci from multiple genetic markers

Question

[garimaprazapati]

I am struggling to analyze a data set of >200 loci gathered from a set of 30 genetic markers. I am learning the software BEAST 2.0. I can't get to the part where I'm supposed to use all the genes and since my data has ambiguities (Y,R etc.), is unphased and

1. I don't understand what to do as when I import it in the nexus format, the tree generated by BEAST shows the two allelic markers of a gene on different clades.
2. I also don't know whether 'concatenation' of all gene sequences is a good idea or not for BEAST analysis.
3. If I import all 30 gene sequences into the software separately and analyze, I get 30 different trees!!!
4. There is very little help available on the internet to help beginners like me for analysis by BEAST software.

I NEED URGENT HELP.

Garima

[GenoMax]

Am not a BEAST user but it looks like there are plenty of tutorials/manuals available for the BEAST v.2.0. Have you tried to work through a tutorial that is similar to the data you are trying to analyze?