SystBiol_TreeData.tar

SystBiol_TreeData.ta

Supplementary Materials

Supplementary material

Amino acid alignment

This is the amino acid alignment used in Rota-Stabelli et al. (in review) Syst. Biol

A set of input tree dataset inferred using RaxMl overlapping on 443 prokaryotic genera taxon set.

This is a directory containing 5 input tree datasets in newick format. Prok_dataset: is composed of input trees overlapping on 443 prokaryotic genera taxon set. Prok_MinusRogue_dataset: The same as Prok dataset except the taxa that were identified as unstable by a concatabomination analysis have been pruned out. Eubac_dataset: Also a subset of Prok, this time with the archaebacterial taxon set pruned out. Eubac_MinusRogue_dataset: A subset of Eubac_dataset with the unstable taxa pruned out. Finally Arc_dataset: Another subset of Prok, this time with all the eubacterial taxon set pruned out

Supplementary Materials

This file include all Supplementary Figures, the Supplementary Figures Captions and Supplementary Table 1

Nucleotide alignment

This is the nucleotide alignment used in Rota-Stabelli e al. (in review Syst. Biol.). It is originally from Regier et al. 2010 - Nature. See Main text for details

MrBayesBlock

Commands used for Bayesian Analyse

suppFigureS2

Supplementary Figure S2. Bayesian, Maximum Likelihood, and Parsimony topologies of the data from Luo et al. (2015). The optimal tree with node support is shown for each method (a-c) as well as the topologies that are produced after nodes with <0.5 support are collapsed to polytomies (d-f), and when nodes with <0.8 support are collapsed (g-i)

suppFigureS1

Supplementary Figure S1. Bayesian, Maximum Likelihood, and Parsimony topologies of the data from Hilton and Bateman (2006). The optimal tree with node support is shown for each method (a-c) as well as the topologies that are produced after nodes with <0.5 support are collapsed to polytomies (d-f), and when nodes with <0.8 support are collapsed (g-i)

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