Question: Multiple sequence alignments CONSIDERING rearrangements and inversions
gravatar for Felix Francis
3.1 years ago by
Felix Francis430
United States/University of Delaware
Felix Francis430 wrote:

Any recommendation for tools capable of doing a multiple (nulceotide)sequence alignment CONSIDERING rearrangements and inversions? pros and cons ?

I came across mauve, gril and mlagan. Are there any others for aligning and identifying more accurately,  the genomic rearrangements of >12 sequences (which are ~60 kb long and not whole genomes) ?

ADD COMMENTlink modified 3.0 years ago by Biostar ♦♦ 20 • written 3.1 years ago by Felix Francis430

Its a bit difficult. I had similar kind of data. I used mauve and then converted the xmfa to phylip/fasta. But the alignment was not reliable at few places. Still you can a give a try.  The scrip I used with options -c -f phylip

ADD REPLYlink written 3.1 years ago by geek_y8.3k
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