gap alignment and local alignment?

[mingkunli]

which software is capable of doing gapped alignment besides SOAP?
which software is capable of doing local alignment that can align different part of read to different ref region?

[lh3]

novoalign and bwa find gaps on single-end reads; maq finds gaps on paired-end reads only. New cross_match is recommended to do local alignment. You may also try ssaha2, shrimp and BFAST(?). If I am right, they all do gapped alignment.

[mingkunli]

thanks, lh3.
Among them, which can take use of quality score? I know your MAQ can, SOAP seems can't(although it can display the quality score).

[andpet]

Mosaik from the Marth Lab also does gapped alignment and uses quality values. It also provides functions like alignment merging, sorting, visualization and is well documented.

Andreas