Could anyone let me know which software I can use to do local alignment of two sequences? Thanks very much!
Maybe you can start with "water" (implementation of Smith and Waterman local alignment) in the EMBOSS package.
In Unbuntu: apt-get install emboss!
Thanks a lot! I should not forget Water! It is very famous!
wikipedia has a comprehensive list
Wikipedia's List of sequence alignment software page is far from comprehensive... but it does provide a reasonable selection of options to start with.
For example: the list is missing some of the EMBOSS alignment programs
The below two pages list several options for aligning two reads.
Thanks so much!
BLAST (ie. BLAST2SEQ)
Edit: I second water too. Its very useful (albeit quite slow...)
Thanks! I get it!
Jalview is a free MSA visualisation software that can generate local alignment within large protein. It offer a range of multiple sequence alignment tools including Clustal Omega, Clustal W, Mafft, Muscle, Tcoffee and Probcons. They have YouTube video playlist about 'Selecting and Editing Sequences using Jalview'.
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