Author: Lars S Jermiin; Renee A Catullo; Barbara R Holland
Title: A new phylogenetic protocol: Dealing with model misspecification and confirmation bias in molecular phylogenetics Document date: 2018_8_27
ID: hr6wfx4g_13
Snippet: Having inferred the phylogeny using model-based phylogenetic methods, it is possible to test the fit between tree, model and data (step 10 of the new protocol). A suitable test of goodness-of fit was proposed in 1993 (172) (Fig. 4) . In brief, using the inferred optimal tree, including the edge lengths, it is possible to simulate data sets under the null model (i.e., the inferred optimal model of sequence evolution with its parameter values inclu.....
Document: Having inferred the phylogeny using model-based phylogenetic methods, it is possible to test the fit between tree, model and data (step 10 of the new protocol). A suitable test of goodness-of fit was proposed in 1993 (172) (Fig. 4) . In brief, using the inferred optimal tree, including the edge lengths, it is possible to simulate data sets under the null model (i.e., the inferred optimal model of sequence evolution with its parameter values included). This is called a parametric bootstrap. Given this tree and this model of sequence evolution, several sequence-generating programs (5,160,173-175) facilitate procurement of pseudo-data.
Search related documents:
Co phrase search for related documents- data set and model base: 1, 2, 3, 4, 5
- data set and new protocol: 1, 2, 3
- data set and null model: 1
- data set and optimal model: 1, 2, 3, 4, 5, 6, 7, 8, 9
- data set and optimal tree: 1, 2
- data set and parameter value: 1
- data set and phylogenetic method: 1, 2, 3, 4
- data set and sequence evolution: 1, 2, 3, 4, 5, 6
- data set and sequence evolution model: 1, 2, 3, 4, 5, 6
- data set and sequence evolution model tree: 1
- data set and sequence evolution optimal model: 1
- data set and suitable test: 1
Co phrase search for related documents, hyperlinks ordered by date