I need to compare some sequences longer than 10Mb. What kind of software is the best for such work? Can I do this work locally (without internet sources)? If I have sequences in FASTAQ format, I need to convert this format in FASTA or the software which able to work with FASTAQ format has already exist?
I used MUMmer before and it gives me pretty good result.
http://mummer.sourceforge.net/
I heard other people use PECAN and MAVID for large scale alignment and get very good result too.
I recommend MAUVE. Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
http://gel.ahabs.wisc.edu/mauve/
I also suggest you to go for either ClustalX or Mauve which is being use for multiple genome alignment.
BioEdit, Mega6, are best for Aligne. Also, you can use MAFT for Aligning.
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