Merge pull request #1 from AidanDelaney/master

Version number in help output
Merge pull request #48 from andrewjpage/master

versioning
Merge pull request #2 from AidanDelaney/master

Python setup.py and general cleanup
split sequence in fasta file over multiple lines
eliminate the requirement for a phylip file for gubbins
integrate fastml
disable timestamp in filenames by default
copy output of fastml for use in gubbins
break output fasta files from fastml over multiple lines
stats for each node
allow for root node to have no distance
filter out internal nodes from output
count number of leaf nodes for phylip
print out number of leaves in phylip
use original snp sites for fastml
check fastml is in PATH
print out all taxons to tab file
dont count gaps in recombination stats
dont list internal nodes in tab file
Merge pull request #50 from andrewjpage/master

Fastml integration