I often use
Jalview for global alignment of proteins or DNA sequences for analyzing homologs, etc. However, I would like to be able to visualize many local alignments at once. For example, if I have a specific gene region, say 20KB, and I know that there are 10 genes within the region, each 1 KB. I would like to be able to input the 20KB region and all 10 genes into Jalview, and conduct local alignments of each gene to the reference at once, so I can see where the genes are aligning to the gene region. Does anyone know how to do this in Jalview in particular? Thanks!
I often use
We are working on supporting exonerate (https://www.ebi.ac.uk/~guy/exonerate/) output in Jalview, and may well provide it as a service in the future. Until then, you could try using one of the alignment services which allows local alignment by setting the 'end gaps' cost to zero (ClustalWS does this, and MAFFT has a local alignment mode too). For DNA, I'd also recommend picking the IDENTITY substitution matrix in ClustalWS since you don't expect much variation.
Jalview's built in alignment algorithms could easily be adapted for this too. I've added a feature request over at http://issues.jalview.org/browse/JAL-1754