# MajorityRuleAndTreeIslands Supplementary data for: Serra Silva, A. and Wilkinson, M. (202#). On defining islands of trees and their effects on consensus. *In prep.* ### Contents of each folder - Data: contains the datamatrix and PAUP* and MrBayes blocks used to run the phylogenetic analyses - PardoPars_Islands.zip: contains the Nexus formatted treefiles containing the TBR/SPR/NNI islands of most parsimonious trees yielded by [Pardo et al.](https://pubmed.ncbi.nlm.nih.gov/28630337/)'s (2017) datamatrix, and the strict and majority-rule consensus of all trees - FirstIsland.tre has 18 trees - SecondIsland.tre has 72 trees - ThirdIsland.tre has 90 trees - FourthIsland.tre has 216 trees - FifthIsland.tre has 486 trees - allTrees\*.tre are the Nexus formatted consensus trees of all 882 most-parsimonious trees \newline - PartitionedByIsland.zip: contains the files needed to run a partitioned by island consensus and its output - Island files also in PardoIslands - consensusBlock.nex contains all the PAUP\* commands needed to run the consensus analyses - Each island has a file with its strict consensus (\*Strict.tre), majority-rule consensus (\*M50.tre) and log (\*.log) \newline - WeightedByIsland.zip: contains the files needed to tun a weighted by island size consensus and its ouptut - Nexus formated island files with each tree weighted inversely to island size (\*Weights.tre) - consensusBlock.nex contains all the PAUP\* commands needed to run the consensus analyses - Files named AllIslands\* correspond to the output files \newline - RarefiedM50.zip: contains the files needed to run a rarefied majority-rule consensus and its output - Island files also in PardoIslands - randomTreeNumbers.R is the random number generator - randTest.txt is the list of random tree numbers - consensusBlock.nex contains all the PAUP\* commands needed to run the consensus analyses of the randomly selected tree numbers - 1000ConsensusTrees contains the output of the majority-rule consensus (Rarefied\*), and a strict (summaryStrict.\*) and majority-rule (summaryM50.\*) summary of the 1000 consensus trees \newline - PardoBayes_1-NNIislands.zip: contains the files needed to extract NNI islands from a Bayesian tree distribution and the NNI islands - PardoCharacters.nex.trprobs is the Bayesian tree distribution from an analysis of [Pardo et al.](https://pubmed.ncbi.nlm.nih.gov/28630337/)'s (2017) datamatrix - nniIslands_PardoBayes_series.R performs the island extraction - nniIslands_PardoBayes_parallel.r performs the island extraction with a parallel implementation - islandFiles contains the NNI islands extracted from the Bayesian tree distribution \newline - PardoPars_12-RFIslands.zip: contains the script to extract 12-RD islands from the MPT distribution (can be edited for the Bayesian extractions) and the 12-RF islands \newline - PardoBayes_x-RFislands.zip: contains the 2- to 12-RF islands extracted from the Bayesian distribution - x-RF folders contain the x-RF islands extracted from the Bayesian tree distribution \newline - MDS.zip: contains the script to run a multidimensional scale analysis of the 1-NNI islands of the Parsimony and Bayesian tree distributions, it also contains the MDS plots \newline - IslandFinder.pas is the source file for a Pascal program that identifies x-RF islands - Program written by Mark Wilkinson - Unlike the islandNeighbours R package it does not generate tree files, rather it recovers island size and the indices (relative to the original tree file) of the trees that make up each island - Usage ./IslandFinder ### Citations If you use the datamatrix please cite: Pardo, J.D., Small, B.J. and Huttenlocker, A.K., 2017. Stem caecilian from the Triassic of Colorado sheds light on the origins of Lissamphibia. Proceedings of the National Academy of Sciences, 114(27), pp.E5389-E5395. ### Problems opening zipped folders If you cannot open the zipped folders, the data is also available through: https://github.com/anaserrasilva/MajorityRuleAndTreeIslands ### Installing *islandNeighbours* To install the package used to extract the NNI islands use: ```r library(devtools) install_github("anaserrasilva/islandNeighbours") library(islandNeighbours) ```