Added function to build hmms.
Made stopping condition in recursive treewalker explicit
Removed 'cute' comments, sorry Shailen.
Minor formatting change to README.
Added Bushra to developer list in README.
Corrected minor error in the README file
Added code to generate MSAs for each node in a tree
Preliminary commit of code to generate msa's for tree nodes
Wrote code to map ids to sequence objects.
Created alignment, tree and new_sequence files.
Created new file for trying out a throw-away brute-force implementation.
Slight formatting change to README