group-to-group two dimensions Dynamic Programing.

Usage 

 % gdp   matrix file  < data  > result

The format of a matrix file is shown as a example matrix file 'matrix_example'.
Plaese see a example matrix file 'matrix_example'.

------ input data format -----------------------------------------

Cut_ratio=80
U,V,S=7,1,1

Seq1=
CSRC (HUMAN):KLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLV
CABL (HUMAN):KLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNL
EPH (HUMAN):VIGEGEFGEVYRGTLRLPSQDCKTVAIKTLKDTSPGGQWWNFLREATIMGQFS

Seq2=
FER (HUMAN):LLGKGNFGEVYKGTLKDKTSVAVKTCKEDLPQELKIKFLQEAKILKQYDHPNI
IR (HUMAN):ELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKGF
CROS (HUMAN):LLGSGAFGEVYEGTAVDILGVGSGEIKVAVKTLKKGSTDQEKIEFLKEAHLM
TRK (HUMAN):ELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTML
BFGFR (HUMAN):PLGEGCFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEME
RET (HUMAN):TLGEGEFGKVVKATAFHLKGRAGYTTVAVKMLKENASPSELRDLLSEFNVLKQ
EGFR (HUMAN):VLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMAS

-------------------------------------------------------------------
You must put a sequence data as "Sequence name:Sequence data"
or ":Sequence data". If no sequence name, ':' is necessary.
You must put return key at the end of sequence.


------ Parameters -------------------------------------------------
Our default parameter set is below.

 Cut_ratio=80
 U,V,S=7,1,1

U,V,S -> First Gap Cost -> U+V
         Not First Gap Cost -> V
         Out Gap Cost -> S
