Multiple sequence alignments CONSIDERING rearrangements and inversions

Question

[Felix Francis]

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)?

[GouthamAtla]

It's 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 script I used https://github.com/lskatz/lskScripts/blob/master/convertAlignment.pl with options -c -f phylip