Question: Recommendations For Dn/Ds Ratio Analyses Software?
4
gravatar for Dj111
3.6 years ago by
Dj11140
Dj11140 wrote:

What are the state of the art programs/libraries for performing dn/ds analyses? I know PAML can do it, but I'm wondering if there are others.

I usually work in C++, so I'm particularly interested interested in C++ libraries - does Seqan or the NCBI C++ toolkit have support for this?

ADD COMMENTlink modified 14 months ago by a1ultima380 • written 3.6 years ago by Dj11140
2
gravatar for Vitis
3.6 years ago by
Vitis1.4k
New York
Vitis1.4k wrote:

I'd recommend HyPhy, which is developed under the essentially same mathematical model of PAML but can do much more. http://www.datam0nk3y.org/hyphy/doku.php

ADD COMMENTlink written 3.6 years ago by Vitis1.4k
2
gravatar for fransua
3.6 years ago by
fransua310
Spain
fransua310 wrote:

you can also use SLR program http://www.ebi.ac.uk/goldman/SLR/ more or less in the same way as PAML.

ADD COMMENTlink written 3.6 years ago by fransua310
1
gravatar for Casey Bergman
3.6 years ago by
Casey Bergman16k
Manchester, UK
Casey Bergman16k wrote:

libsequence provides hueristic Ka/Ks functions in C++. You could also look into in Bio++ which states that it has rate estimation routines, but I have not used it myself and can't confirm that this would be useful for you.

ADD COMMENTlink written 3.6 years ago by Casey Bergman16k
0
gravatar for a1ultima
14 months ago by
a1ultima380
London
a1ultima380 wrote:

Here are my recommendations for software ordered by how flexible they are:

  • MATLAB's Bioinformatics Toolbox: Here you have the greatest variety of alternative algorithms, operating system compatibility, sliding vs. whole protein analysis, API to Genbank, etc (Here's a great tutorial for using their dN/dS tool). Just remember MATLAB is not free.
  • KaKs Calculator: If you only care about whole protein dN/dS, many options are available with the Ka/Ks calculator - they also compute statistical significance using Fisher's exact test. I can also provide an R script that generates error bars from the output, just ask.
  • PAML: If you have >2 sequences per protein that you wish to get a dN/dS value from, then many options are available with PAML. This is often used in published papers, but it's not recommended if you only have a pair of sequences per protein.
ADD COMMENTlink written 14 months ago by a1ultima380
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