Multiple Sequence Alignment Program for Protein (for MSF format)


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You have three algorithms. You must choose one for your use.

(1) gtoa2 < data | dist_a [option1][option2] | align_a 1 [option1] | atog1 > result
(2) gtoa2 < data | dist_a [option1][option2] | align_a 2 [option1] | atog1 > result
(3) gtoa2 < data | dist_a [option1][option2] | align_a 3 [option1] | atog1 > result

(1)Tree-based Method
(2)Tree-based Round-robin Method
(3)Tree-based Round-robin Iterative Method

(1) aligns roughly but very fast.
(2) aligns well but needs times a little.
(3) aligns very well but needs times.

(3) is the best algolithm.
If your data is small or if you have enough time,please use it.

If your data is too big or if you don't have enough time,
please use (2).


------ Parameters -------------------------------------------------
CutM -> Cut Ratio of Dynamic Programing at Tree-based Method

CutI -> Cut Ratio of Dynamic Programing at Round-robin Method 
        and Round-robin Iterative Method

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

Default Parameters
CutM=80
CutI=90
U,V,S=7,1,1

You can change those parameters by options2 [-mN1 -iN2 -uN3 -vN4 -sN5].
CutM=N1
CutI=N2
U,V,S=N3,N4,N5


You can also change a matrix by option1 [-f matrix].
The format of a matrix file is shown as a example matrix file 'matrix_example'.
Plaese see a example matrix file 'matrix_example'.
We use 'matrix_amino.c' (PAM250) as a default matrix.
