Carnivore_and_Metazoan_datasets

This zip file contain the input trees, in newick format, used in a supertree analysis to infer the metazoan phylogenetic supertree. It also contains 10 carnivore input tree datasets, in newick format, that were used in a supertree analysis to reconstruct the phylogenetic supertree for the Carnivores

Flowchart of the <i>PhyQuart</i> algorithm.

<p>Simplified flowchart showing a) each of the three possible quartet relationships for a set of 4 sequences (<i>q</i>₁, <i>q</i>₂, <i>q</i>₃), b) the site-pattern classification of observed (<i>N</i>_<i>obs</i>) symmetric () and asymmetric () support (), c) the determination of plesiomorphic (old) split-supporting site-patterns given two different polarities of character transformation along the internal branch of each possible quartet tree, and , and d) estimation of expected convergent split-supporting site-patterns () supporting quartet <i>q</i>₁ in ML split pattern estimations using branch length and model optimization on constraint topologies of the other two possible quartet relationships (<i>q</i>₂, <i>q</i>₃).</p

Quartet reconstruction success given stepwise elongation of one or three terminal branches if sequence lengths equal 250 kbp.

<p>Reconstruction success of <i>PhyQuart</i> (blue) and ML (green) for different rate heterogeneities under different lengths of a) a single long terminal branch (BL2, x-axis) and b) three long terminal branches (BL2, x-axis), given 100 data replicates (y-axis) of 250 kbp length and a fixed alternative internal branch length of BL1 = {0.01}, summarized for <i>α</i> = {0.1, 0.3, 0.5, 0.7, 1.0, 2.0}. A detailed overview of all simulation results of both setups is given as supplementary information <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0183393#pone.0183393.s004" target="_blank">S4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0183393#pone.0183393.s005" target="_blank">S5</a> Figs.</p

Defined model parameters for data simulation (INDELible) and ML analyses used in <i>PhyQuart</i> and PhyML.

<p>Defined model parameters for data simulation (INDELible) and ML analyses used in <i>PhyQuart</i> and PhyML.</p

Quartet simulation setups.

<p>Simulation setups for quartet analyses testing effects of given a very short internal branch (BL1) with a) stepwise elongation of two adjacent (Farris-topology, left) and non-adjacent (Felsenstein-topology, right) terminal long branches (BL2), b) elongation of one terminal branch (BL2) using different lengths for one of the three short branches (BL3), and c) stepwise elongation of three terminal branches, with different lengths of the remaining short terminal branch (BL3).</p

Quartet reconstruction success given stepwise elongation of two terminal branches if sequence lengths equal 250 kbp.

<p>Plots visualizing the reconstruction success of <i>PhyQuart</i> (blue) and ML (green) given stepwise elongation of two terminal branches (BL2, x-axis) and a fixed, very short internal branch length (BL1 = {0.01}) for 100 (250 kbp long) data replicates (y-axis). The plots present the summarized reconstruction success for (a) Felsenstein-, and (b) Farris-topologies of given <i>α</i> = {0.1, 0.3, 0.5, 0.7, 1.0, 2.0} and an invariable site proportion (I) of 0.3. A detailed overview of all simulation results of this setup is given as supplementary information <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0183393#pone.0183393.s001" target="_blank">S1 Fig</a>.</p

29_alns_cut.tar

The genes used to make the 29BAE dataset, after masking of poorly-aligning and uninformative sites

64_singles.tar

The genes used to make the 64AE dataset, after masking of poorly-aligning and uninformative sites

29_aeb

Concatenation of 29 genes conserved in Bacteria, Archaea and eukaryotes

newick_trees.tar

Newick tree files corresponding to Figures 1 and 2 of the article