Align genome clusters with uo to 100kb in size each

Question

[csag6433]

Hi.

im trying to align 30 clusters each about 100 kb in size. since my computer is not that fast i had great success with kalign online so far . it doesnt support filesizes over 2mb tho. can somebody recommend another well working online site for multiple sequence alignment . unfortunately i always get errors with clustal online .

[Joe]

I've tried to do similar things to this in the past. Unfortunately multiple alignment of long sequences is still functionally impossible.

You can do pairwise alignments, and kalign is one of the tools I've also found capable of this (just about). You could also look at LASTZ and mummer but this won't give you multiple alignment.

What are you actually trying to do/show? Alignment may not be the best approach.