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https://forum.ugene.net/forum/YaBB.pl General Category >> Feature Requests >> GPU-Mummer https://forum.ugene.net/forum/YaBB.pl?num=1288166920 Message started by Jai on Oct 27^th, 2010 at 3:08pm

Title: GPU-Mummer
Post by Jai on Oct 27^th, 2010 at 3:08pm

Addition of Mummer ported to GPU (GPU-mummer) for whole genome alignment and analysis would be an extremely useful tool in Ugene.

Title: Re: GPU-Mummer
Post by Mikhail Fursov on Oct 28^th, 2010 at 6:38pm

Jai wrote on Oct 27^th, 2010 at 3:08pm:

Addition of Mummer ported to GPU (GPU-mummer) for whole genome alignment and analysis would be an extremely useful tool in Ugene.

Ok! We will add it to the our TODO feature list.

Title: Re: GPU-Mummer
Post by Alvarenga on Dec 16^th, 2011 at 9:05pm

Hi! How is the addition of this feature going? A genome aligner would be a great addition to UGENE!

I found Mugsy, which also uses Nucmer:
http://bioinformatics.oxfordjournals.org/content/27/3/334.full
http://mugsy.sourceforge.net/

Its advantadge is that it's more automated than MUMmer (we just need to run one command) and it has scripts to transform from .delta to .maf and from .maf to .fasta. It's licensed under GPL.