Question: Multiple sequence alignments CONSIDERING rearrangements and inversions
0
gravatar for Felix Francis
3.3 years ago by
Felix Francis440
United States/University of Delaware
Felix Francis440 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 3.3 years ago by Biostar ♦♦ 20 • written 3.3 years ago by Felix Francis440
1

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 https://github.com/lskatz/lskScripts/blob/master/convertAlignment.pl with options -c -f phylip

ADD REPLYlink written 3.3 years ago by geek_y8.6k
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