Helllo, does anyone know which method and software is best for the detection of saturation of amino acid alignment and nucleotide saturation? And if the saturation is detected, how can I utilize the result to make accurate alignment? Thanks for your help in advance!
Dear Tree Happy
Very good one from Shaban. I was wondering if you are interested in finding dA/dA synonymous and nonsynomymous substitutions as well, whilst checking the alignment.
If so, you may have to go beyond the existing tools like TRanslatorX
Best,
Prash
In DAMBE, load the alignment, and under the "graphics" pull-down menu there is Transitions and transversions vs pairwise distances. This plot is very useful in determining if a set of sequences in a multiple sequence alignment includes distances that are beyond saturation of silent sites with mutations. The attached figure shows the results of analyzing genomes of primate lentiviruses (HIVs and SIVs), as an example. The distances between viruses such as HIV-1 and SIV from colobus monkeys are far beyond saturation, while distances between any two HIV-1 M group viruses are not so great and are not saturated.
Thanks Shaban! But I can not download the pdf file you provided! The downloaded pdf file was always damaged. Could you please provide the name of the article! Thanks very much your help!
Thanks Prashanth! I was not insterested in da/ds now. But perhaps in other research later, I will try the TRanslatorX. Thanks for your help!
Thanks Shaban ! You do not need to provided the title of the aticle any more, I have already downloaded this file. Perhaps it was the internetwork's reason that I could not download this file last time! Thanks again for you kind help!
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