README

README file describing the contents of the supplementary material

Online-Only Supplementary Materials

The online-only supplement of the manuscrip

Additional file 1 of Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction

Supplementary.pdf. The Supplementary Material for the paper. (PDF 426 KB

Human Alu Files

Files related to the Human Alu dataset used in the manuscrip

Supplementary Online Material

This files includes supplementary material, including extra set of results, the model species trees used for simulation (as pdf), and the description of the exact commands used in the simulation study

Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction

<div><p>Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications. This issue has been long recognized; however, whether the potential for discordance between the species tree and gene trees impacts methods of rooting a phylogenetic tree has not been extensively studied. In this paper, we introduce a new method of rooting a tree based on its branch length distribution; our method, which minimizes the variance of root to tip distances, is inspired by the traditional midpoint rerooting and is justified when deviations from the strict molecular clock are random. Like midpoint rerooting, the method can be implemented in a linear time algorithm. In extensive simulations that consider discordance between gene trees and the species tree, we show that the new method is more accurate than midpoint rerooting, but its relative accuracy compared to using outgroups to root gene trees depends on the size of the dataset and levels of deviations from the strict clock. We show high levels of error for all methods of rooting estimated gene trees due to factors that include effects of gene tree discordance, deviations from the clock, and gene tree estimation error. Our simulations, however, did not reveal significant differences between two equivalent methods for species tree estimation that use rooted and unrooted input, namely, STAR and NJst. Nevertheless, our results point to limitations of existing scalable rooting methods.</p></div

Species tree estimation accuracy using rooted and unrooted gene trees.

<p>Species tree estimation accuracy using rooted and unrooted gene trees.</p

Running time of MP and MV.

<p>A: comparison of our implementation of MV/MP with the implementation of MP in Dendropy, which employs a quadratic algorithm, on datasets D1, D2, and D3 with up to 5,000 leaves; B: Linear time scaling of our implementation, tested on the RNASim dataset with up to 200,000 leaves.</p

Absolute triplet distance as a function of the number of taxa.

<p>A: Results from D1, D2, and D3 are combined in one figure; 30 on the x-axis corresponds to D1, 2000 and 5000 to D2, and the remaining cases to D3. For D1 and D2, we fixed R/C = 1 and the clock divergence parameter to medium to best match the conditions of D3. B: Results for D1 and D2 with R/C = 1 and difference levels of clock divergence.</p

Biological

Biological datasets. For Song et al 2012 biological dataset, gene trees, in addition to MRL and MP-EST species trees are included