Muttui

* Added functions to extract genes from a GFF
* Added option --synonymous to only output synonymous mutations
* Added option --strand_bias to output transcription strand information
* Added option -g to take a GFF file - required for --synonymous and --strand_bias
* Added filter function to extract double substitutions and remove mutations at the ends of the genome or not involving 2 nucleotides (previously done separately)

* Updated input to take branch_mutations.txt file from treetime rather than annotated_tree.nex
* Updated all functions to run on this input

* First MutTui release
* Includes reading the annotated tree in from treetime