Profile cover photo
Profile photo
nicolas lartillot
62 followers
62 followers
About
nicolas's posts

Post has attachment
Site-specific selection and evolutionary distances
Coming back the Microsporidia example, the LG model does not just give an artifactual position for Microsporidia. It also gives an estimate for the total tree length of about 10.3 amino-acid changes per site. On the same dataset, CAT-GTR, which accounts for...

Post has attachment
Second-order amino-acid replacement processes
As I mentioned earlier, classical amino-acid replacement matrices indirectly encode site-specific amino-acid preferences in their first-order Markov dependencies, and this is optimal in a low saturation regime. Now, this suggests that we could derive second...

Post has attachment
Second-order amino-acid replacement processes
As I mentioned earlier, classical amino-acid replacement matrices indirectly encode site-specific amino-acid preferences in their first-order Markov dependencies, and this is optimal in a low saturation regime. Now, this suggests that we could derive second...

Post has attachment
The effective number of amino-acids per site
As we have seen, a fundamental consequence of site-specific selective constraints is that the number of amino-acids allowed at each site is typically much smaller than 20. This in turn results in a purely combinatorial effect: few amino-acids per site means...

Post has attachment
Site-specific selection and phylogenetic accuracy
In my last post , I argued that classical amino-acid replacement matrices do not faithfully describe the long-term evolutionary process at typical positions of protein-coding sequences. More specifically, those matrices do not correctly capture the long-run...

Post has attachment
Double standard (2)
Just a side remark: in my last post, I pointed out that classical amino-acid replacement matrices implicitly encode site-specific selection in the first-order Markov dependencies of the process, and that doing so is optimal in situations of low sequence div...

Post has attachment
Long-term site-specific selective constraints
There is a catch in my argument about the  double standards   of some of the current phylogenetic models, concerning rate- versus pattern-heterogeneity across sites. It is unfair to suggest that a model does not model the consequences of varying selection a...

Post has attachment
Double standard
Nobody today would publish a phylogeny that has been inferred using a model that does not account for rate variation across sites, at least not a phylogeny over a large evolutionary scale (e.g. animals, eukaryotes, etc). And indeed, using such rates-across-...

Post has attachment
Ctenophores and the role of models in phylogenetics
First of all, I gave a phyloseminar last week, on the problem of dealing with patter-heterogeneity across sites in phylogenetic inference. I find this idea of phyloseminars really neat. Many thanks (and kudos) to Erick Matsen, for organizing all this. There...

Post has attachment
Resurrection
This blog has been silent for such a long time (two years…). But there are quite a few things I would like to share with you, concerning various current developments in phylogenetics and in Bayesian inference. So, let start it up again.
Wait while more posts are being loaded