Merge pull request #56 from andrewjpage/master

update test files
Merge pull request #57 from andrewjpage/master

unquote tree nodes for fastml and check if too much is filtered out
Merge pull request #58 from andrewjpage/master

missing comma
Merge pull request #59 from andrewjpage/master

remove filtered sequences from starting tree
Merge pull request #60 from andrewjpage/master

pairwise
Merge pull request #61 from andrewjpage/master

Gaps can be in ref as well as alt
swap branch snp bases
remove double dot in filename