Merge pull request #70 from andrewjpage/master

Use bases for gaps for internal nodes after fastml
Merge pull request #71 from andrewjpage/master

reroot on outgroup should keep internal nodes
move block inwards until likelihood stops improving
fix rerooting on outgroups
more like original pattern
pass around likelihood of blocks and block size
speedup searching for next snp
reduce search space for counting block size
add likelihood to blocks
reduce end window search space
Merge pull request #72 from andrewjpage/improving_likelihood

Improving likelihood
filter out identical blocks
recalc block size
rewind to last snp
move end to last snp
Merge pull request #73 from andrewjpage/improving_likelihood

Improving likelihood
part4 log10
Merge pull request #74 from andrewjpage/improving_likelihood

part4 log10