Optimising alignment speed

Wise2 assummes you have a rather small amount of memory (20 MBytes). When it is making an alignment, if it cannot make the explicit matrix in that size (being length of query $\times$ length of target $\times$ state number) it has to move to linear memory (length of query $\times$ state number). The linear memory is much slower (it is the one that starts with ``Find start end points'').

If you have more memory than 20 Mbytes, then it is really sensible to up the number, using the -kbyte option. For a machine with say 64Mbytes physical memory I would suggest putting an upper limit of 50Mbytes with -kbyte. This does assumme you are not using it for anything else.

You can change the compile time default in basematrix.h if you can't be bothered to remember to change it every time