Deleted many unused fcts. Added some stuff.

 On branch master
 Changes to be committed:
   (use "git reset HEAD <file>..." to unstage)

	modified:   fasta.py
        -Added Stockholm Parser
        -Added a function to remove sequence gaps

	modified:   fullmsa.py
        -Changed sca5 to use a kwarg for the bgq
         bgq now defaults to using estimateBGFreq
         the keyward to specify a custom bgq is 'bgq'

	modified:   pinfwrapper.py
        -Rewrote to load the dynamic c-libraries from the
         same directory that the rest of pysca lives in.
	modified:   pysca.py
        -Deleted some unused functions
        -Modified register to jive with the new version of
         water.align
	modified:   water.py
        -Removed __many__ unused functions
        -Rewrote water.align such that it no longer utilizes
         temporary files. Temporary files are for chumps.
         Pipes 4ever.