changed log calculation

*The log is no longer calculated in the kmeans function, this is now
done as part of the parsing step in phyml, and automatically part of
the output of raxml. This allows us to not have to convert raxml site
likelihoods from log to antilog and back to log
likelihood_parser() now returns log likelihoods instead of likelihoods

*to maintain consistency with the raxml output, the phyml output is now
log likelihoods
removed antilog calculation

* intitially the antilog of each log likelihood was taken for input
into kmeans which would then take the log again, since log likelihoods
are what we estimate kmeans from, we took away those two redundant steps