Showing posts with label models of evolution. Show all posts
Showing posts with label models of evolution. Show all posts
Friday, April 7, 2017

Parsimony versus models for morphological data: a recent paper

›
I have written on this blog before about the use of likelihood or Bayesian phylogenetics for morphological data . In our journal club this w...
5 comments:
Saturday, February 18, 2017

Robert Lanfear on the state of molecular phylogenetics

›
I had hoped to write this up earlier, but there we are. On 9 February I went to a presentation by Robert Lanfear , the author among other th...
Sunday, December 11, 2016

Cladistics textbook, part 2

›
Coming back to the textbook Kitching IJ, Forey PL, Humphries CJ, Williams DM, 1998. Cladistics second edition - the theory and practice of...
Saturday, December 3, 2016

Molecular clock models in three different programs

›
There are quite a few molecular clock models implemented in various phylogenetic programs. What I find somewhat annoying is that there is ge...
Wednesday, November 30, 2016

Hey, since when can RAxML do that?

›
Maybe I missed something, but I only noticed today that the super-fast likelihood phylogenetics software RAxML can use four different models...
Thursday, November 17, 2016

Clock rooting with strong rate shifts - or not

›
Today at our journal club we discussed Schmitt 2016, "Hennig, Ax, and present-day mainstream cladistics, on polarising characters"...
Friday, November 4, 2016

CBA seminar on molecular phylogenetics

›
Today I went to a Centre of Biodiversity Analysis seminar over at the Australian National University: Prof. Lindell Bromham on Reading the s...
Sunday, July 3, 2016

The Markov k model for discrete mophological data

›
The most frequently used model of character evolution for morphological data is called the Markov k (Mk) model. It was suggested by Lewis ( ...
2 comments:
Sunday, June 26, 2016

Implementation of substitution models in phylogenetic software

›
Concluding the little series of posts on nucleotide substitution models, below is a summary of my current understanding of how to set sever...
Friday, June 24, 2016

What number of schemes to test to get what substitution models in jModelTest

›
Another thing that occurred to me that might be useful to write about in the context of substitution models concerns jModelTest. The back...
Thursday, June 23, 2016

Overview over the substitution models

›
Continuing from the previous post , here is a run-down of the commonly used models, their abbreviations, alternative names and abbreviations...
Tuesday, June 21, 2016

Nucleotide substitution models

›
I recently had reason to consider alternative nucleotide substitution models and got a bit frustrated at the scarcity of clear, easily under...