What I am stating here is pretty much a textbook problem so please do not be offended if you find it too trivial. I have never been into phylogenetics but at the moment, I need to make a phylogenetic tree for a gene family of interest.
I extracted the sequences for this gene from different bacterial genomes, aligned the sequences and now I am ready to start. I looked at the available programs and there are just too many of them. For some reason, I liked PHYLIP. So I started to use it.
What I propose to do is the following: Use the alignment to build tree using distance based method (both NJ and UPGMA) and see if they both produce the same tree. If that is the case, I should be happy with the same and use this tree. If not, then I might need to explore Parsimony or Likelihood based methods. However, from whatever I have read so far, I understand that these methods run longer to run and sometimes, they do not even converge. I actually did try using dnapenny program from Phylip package and got the message "search broken off" after the program had been running for a couple of hours atleast. Any feedback/suggestions with my problems will be highly appreciated.
Thanks and regards, Mark.