Showing posts with label methods. Show all posts
Showing posts with label methods. Show all posts
Thursday, September 26, 2019

Incongruence Length Difference test in TNT

›
Because I am fed up with figuring it out anew every time I need to use the Incongruence Length Difference (ILD) test (Farris et al., 1994) i...
Friday, April 20, 2018

Time-calibrated or at least ultrametric trees with the R package ape: an overview

›
I had reason today to look into time-calibrating phylogenetic trees again, specifically trees that are so large that Bayesian approaches are...
1 comment:
Monday, April 2, 2018

How problematic is the jump dispersal parameter in ancestral area inference?

›
I recently read an article in the Journal of Biogeography titled "Conceptual and statistical problems with the DEC + J model of fou...
Saturday, January 27, 2018

Bioregionalisation part 3: clustering with Biodiverse

›
Biodiverse is a software for spatial analysis of biodiversity, in particular for calculating diversity scores for regions and for bioregion...
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:
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...
Tuesday, July 19, 2016

I must be missing something

›
As I continue to contemplate Ebach and Michael's recent paper From Correlation to Causation: What Do We Need in the Historical Science...
Wednesday, July 13, 2016

Experimental versus historical science

›
Long time no blog; it seems to come to me in bursts. Anyway, a colleague has drawn my attention to a paper that has recently appeared, From...
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...