First commit
modified to produce alignments for each family rather than just a list
modified to avoid deleting original file.

If original is given as input, '-formatted' is automatically added.

If formatted version not found, it prints a nice reminder to format the document using papers
Added a few more conversions so that tables can be inserted into documents

The following substitutions were added (along with proper documentation at the top of the script:

- \t is converted to & (used as column separator in tables; must have spaces on either side)
- \[ ... \] is converted to { ... } (used because Papers uses curly braces for citations)
- /begin converted to \begin (used because \begin screws up Papers)
- /end converted to \end (used because \end screws up Papers)