README
+++++++++++++++++++++++++++++++++++++++
+ FORMAT *.fasta for Needleman Wunsch +
+++++++++++++++++++++++++++++++++++++++
+++++++++++++++ START OF FILE ## no newline allowed
>header1 ## newline allowed
SEQUENCE ## newline allowed, characters that occur in the *.matrix file are allowed
>header2
SEQUENCE
>header3... ##the rest of the sequences will not be considered!
...
++++++++++++++++++++++++++++++++++++++++
+ FORMAT *.matrix for Needleman Wunsch +
++++++++++++++++++++++++++++++++++++++++
EXAMPLE: all tab delimited \t
++++++++++++++++++++++++++++++++++++++++++ START OF FILE ## no newline
A C G T
A 10 -5 -5 -5
C -5 10 -5 -5
G -5 -5 10 -5
T -5 -5 -5 10
++++++++++++++++++++++++++++++++++++++++++++++
+ FORMAT *.asp for Manhattan Tourist Problem +
++++++++++++++++++++++++++++++++++++++++++++++
EXAMPLE: values in matrix are tab delimited \t, no blank lines!
DIMENSION: size (n & m) of matrix is variable,
BUT: G-diag: n x n G_right: m x n G_down: n x m
+++++++++++++++++++++++++++++++++++++++++ START OF FILE ## no newline
G_down: 5 6
0.32 0.60 0.76 0.73 0.80 0.56
0.97 0.43 0.50 0.25 0.89 0.20
0.39 0.42 0.31 0.94 0.31 0.21
0.20 0.81 0.41 0.96 0.90 0.83
0.86 0.15 0.49 0.70 0.54 0.84
--- ## these lines are ignored
G_right: 6 5
0.32 0.60 0.76 0.73 0.80
0.97 0.43 0.50 0.25 0.89
0.39 0.42 0.31 0.94 0.31
0.20 0.81 0.41 0.96 0.90
0.86 0.15 0.49 0.70 0.54
0.20 0.81 0.41 0.96 0.90
---
G_diag: 5 5
0.32 0.60 0.76 0.73 0.80
0.97 0.43 0.50 0.25 0.89
0.39 0.42 0.31 0.94 0.31
0.20 0.81 0.41 0.96 0.90
0.86 0.15 0.49 0.70 0.54
---
### file should stop here!
