cleaned up code

* got rid of unnecessary imports and made changes according to
recommendations from pylint and pep8
modified error exception to be more specific

* Former exception just caught a phylogeny program error then allowed
the program to continue. This searches the output of either raxml or
phyml to determine if we are excepting the correct error
added stderr and stdout to PhymlError

* This allows us to parse the output for more specific error exceptions
added stderr and stdout to RaxmlError

* This allows us to parse the output for more specific error exceptions