Minor change
Added codon_partition
Added functions for partitioning by codon

— getPartitions, uses the list of alignments and their gene names to
assert whether they should be codon partitioned or not, it then returns
the numbers for each partition
— partitionCodon: uses a ORF finder to work out the frame and then
returns an alignment and a list of 3s.
— TODO — this will need changed, doesn’t work. I have to upload it on
github cos my mac is about to run out of power.
Updated given changes to tools
Added codon_partition