moved the write_phylip function to Heathpy so it can be used in other applications
added write_phylip function to write alignment in custom phylip format

this format allows names longer than 10 characters and is not interleaved
it would be the equivaled of 'phylip-relaxed-sequential' in biopython if such a thing existed
commented out line that converts start to zero-based counting.

This does not seem to be necessary for bioperl and was giving incorrect results. It is
now giving correct results, tho I keep the line in case I need to revert it for any reason
first commit
Added function to identify C-terminal CaaX domains in DNA sequences

This motif is characteristic of the pheromone genes in basidiomycete B locus mating type
loci. It can be used to identify pheromone genes on the same contig as the pheromone
receptor gene

In addition to find_CaaX, I also wrote a function called six_frame_translation that is
used by find_CaaX to translate a DNA sequence in all possible reading frames.

find_CaaX could be fairly easily generalized to find any sequence motif passed to the
function, but I was in a hurry so I didn't bother to write it this way
first commit