orQuartets: Partition and Quartet similarity counts for trees generated...

In ms609/OReillyEtAl2016: Distance metrics for trees generated by O'Reilly et al. 2016

Partition and Quartet similarity counts for trees generated from the datasets of O'Reilly et al.

Description

For each of the 3000 matrices simulated by O'Reilly et al. (2016),, I conducted phylogenetic analysis under different methods:

Usage

orQuartets

orPartitions

Format

An object of class list of length 3.

Details

• markovUsing the Markov K model in MrBayes.

• equalUsing equal weights in TNT.

• implied1,implied2,implied3,implied5,implied10Using implied weights in TNT, with the concavity constant (k) set to 1, 2, 3, 5, or 10

• impliedCBy taking the strict consensus of all trees recovered by implied weights parsimony analysis under the k values 2, 3, 5 and 10 (but not 1).

For each analysis, I recorded the strict consensus of all optimal trees, and also the consensus of trees that were suboptimal by a specified degree.

I then calculated, of the total number of < reference tree, how many were the same or different in the tree that resulted from the phylogenetic analysis, and how many were not resolved in this tree (r2).

The data object contains a list whose elements are named after the methods, as listed above.

Each list entry is a three-dimensional array, whose dimensions are:

• 1The suboptimality of the tree: for markov, the consensus at a 50 52.5 all trees that are 0, 1, .... 19, 20 steps less optimal than the optimal tree; for implied, the consensus of all trees that are 0.73^(19:0) less optimal than the optimal tree.

• 2The number of < in the estimated tree but not the generative tree (= 0), resolved in the generative tree but not the estimated tree

• 3The number of the matrix, from 1 to 100.

Source

\insertRef

Congreve2016Quartet

See Also

clMatrices, clReferenceTree.

ms609/OReillyEtAl2016 documentation built on March 3, 2024, 1:18 p.m.