I'm trying to automate (and improve) a computational 'procedure' in my new lab (of traditional biologists) and I'm having trouble replicating a step.
At one point in an analysis they use the GUI version of MUSCLE to align a set of sequences and then generate a UPGMA tree. Then they save the pairwise distance matrix for downstream analysis. I've already automated the downstream and upstream processes but I'm having trouble with this step.
The MUSCLE command line doesn't have an option for returning the pairwise distances (only the final tree). Is there a way to get those distances out? Or is there a way to extract the distances from the tree (a simple googleing didn't reveal anything)? Or is there a way to calculate those distances myself (the muscle manual doesn't give much help explaining how it arrives at the distances)? Or any other suggestions? I really don't want to resort to some silly 'automated GUI interaction' just to get this output data.