Thread: [Mauve-users] progressiveMauve works on DNA or AA?
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From: Uwe M. <uwe...@sl...> - 2017-03-08 12:15:46
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Dear list, as a newbie: how do I find out if progressiveMauve works on DNA or AA? The format specification provided is for DNA. On the other hand, Mauve uses Clustal and muscle alignment tools ... Thanks! |
From: Aaron D. <aar...@ut...> - 2017-03-08 22:12:17
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Hi Uwe, this information might only be implicit in the documentation. Despite its use of MUSCLE, progressiveMauve only computes DNA-level genome alignments. I am not aware of any software to compute protein- level genome alignments (though it's been a while since I looked around), possibly because the concept of a positional homology genome alignment becomes less useful at the high levels of evolutionary divergence that would require a switch to amino acid alignment. For pairwise genome alignment there is a protein mode in MUMmer. For multiple genomes you might look at gene family clustering approaches. -Aaron On Wed, 2017-03-08 at 13:00 +0100, Uwe Menzel wrote: > Dear list, > > as a newbie: how do I find out if progressiveMauve works on DNA or > AA? > The format specification provided is for DNA. > On the other hand, Mauve uses Clustal and muscle alignment tools ... > > Thanks! > > > ------------------------------------------------------------------- > ----------- > Announcing the Oxford Dictionaries API! The API offers world-renowned > dictionary content that is easy and intuitive to access. Sign up for > an > account today to start using our lexical data to power your apps and > projects. Get started today and enter our developer competition. > http://sdm.link/oxford > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. |