In a recent post, Dan Graur made various criticism to a paper publish last year in PloS One:
and here is the link to the paper:
I like the concept of this paper, which is mixing various bioinformatics methods to identify evolutionary pressures on sites and trying to correlate them with disease mutations (see also our review on the subject (http://www.biochemj.org/bj/449/bj4490581.htm) and this recent one (www.sciencedirect.com/science/article/pii/S0022283613004464#) )
I have other comments (more recommendation) I would like to share in this blog:
- They used alignment from ClustalW, which is surprising as it is the oldest of these methods. Better methods have been publish since them, one can cite Muscle, Mafft, Probcons, T-coffee and Clustal-Omega. The authors compared some of them, but found that ClustalW was the best to use in their study. They could also have tried some phylogeny-aware method to align (PRANK, PAGAN), to see if it makes a difference or not.