As per Simon's request I have added a simple standard batch file (available with builds after Feb 1st) to look for a single recombination breakpoint.

The algorithm is simple:

Using NJ (with TN93) reconstructed trees we

• Fit a single tree to the whole alignment, using a user selected model
  
• Try to break the alignment at every variable site and fit two separately inferred trees (again, NJ) using the same model (with global parameters shared, but branch lengths inferred independently).
  
• Measure goodness of fit by AIC
  

If the analysis finds a putative breakpoint, more rigorous tests (e.g. KH test - a standard analysis) can be used to assess the significance of phylogenetic incongruence.

This analysis can compensate for rate variation (using an appropriate substitution model) and use codon models for cDNA.

Dear Sergei,

Seems to work well. A few suggestions:

1. Rather than fit a model as part of the analysis, could a previously fitted model be loaded instead? Perhaps the recombination analysis could also be added to the result processor module.
2. More output would be nice: how about a table with the breakpoints, the AIC, the delta AIC, with optionally, the trees for each partition, a KH test for the significance of the difference in trees, and some tree distance measures. It might also be good to tally the sites that are contributing to the conflicting phylogenetic signal, but I'd have to think a bit how best to present these.

Best,
Simon