Protein Family Alignment Annotation Tool svncode

add support for shannon and different matrices

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small changes to improve memory

various

added comments

forget what I changed here

various changes included vne diagonal weighting

shannon does not need to set equal weight. as the identity matrix already takes care of this

fix bug where too much weight was given to diagonals in vne and it was similar to shannon

"load HSSP files as pfaat alignments"