Multiple sequence alignment program using random iterative algorithm .

    b_m_1      : Random iterative algorithm with single-type partitioning.

    b_m_1_as   : Random iterative algorithm with single-type partitioning.
                 The iteration terminates when all possible partitions give 
                 no improvement. 

    b_m_2      : Random iterative algorithm with double-type partitioning.

    b_m_2_as   : Random iterative algorithm with double-type partitioning.
                 The iteration terminates when all possible partitions give 
                 no improvement. 

    b_m_all    : Random iterative algorithm with random partitioning.

    b_m_all_as : Random iterative algorithm with random partitioning.
                 The iteration terminates when all possible partitions give 
                 no improvement. 

    b_m_t      : Random iterative algorithm with tree-dependent partitioning.

    b_m_t_as   : Random iterative algorithm with tree-dependent partitioning.
                 The iteration terminates when all possible partitions give 
                 no improvement. 


Usage 

 % program name   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 -----------------------------------------
CutM=80
U,V,S=7,1,1
Seed=1
Stop=10

Seq=
CSRC (HUMAN):KLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLV
CABL (HUMAN):KLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNL
EPH (HUMAN):VIGEGEFGEVYRGTLRLPSQDCKTVAIKTLKDTSPGGQWWNFLREATIMGQFS
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.

CutM=80
U,V,S=7,1,1       U,V,S=7,1,1
Seed=1
Stop=10

U,V,S -> First Gap Cost -> U+V
         Not First Gap Cost -> V
         Out Gap Cost -> S
Seed  -> Seed of random number . Random number is used for partitioning.
Stop  -> Required for b_m_1, b_m_2, b_m_all, b_m_t.
         The iteration terminates when number of partitions reaches this 
         value.
