I am in need of some help again.
I have a set of sequences (in a multifasta file), and I need to align them against a reference with local alinment. I have tried EMBL-EBI pairwise alignment tools, but it just calculate the local alignment of two sequences. And 'bwa mem' does a local alignment, it only aligns the best matching parts of my contigs while the remainder is clipped off, but I need the intact sequences. Other software that can be useful?
Thanks in advance.