Data and materials for: "Convergence of Ion Channel Genome Content in Early Animal Evolution" Benjamin J. Liebeskind, David M. Hillis, Harold H. Zakon This archive includes all the materials and data files for running the analyses described in the paper. The custom scripts used for the analysis are available at: https://github.com/bliebeskind. The material is presented below in workflow order and the relevent scripts will be referenced throughout. If you use these scripts or datasets, please cite the paper above (thanks!) There are three folders: Sequences_and_Alignments: input for Evolmap and Notung analyses. RawOutput: trees, and output from EvolMap and Notung. Ancestor_Analysis: parsed results and PCA. Sequences_and_Alignments: EvolMap_fastas.zip: unaligned sequences used as input for EvolMap. SimTrim_alignment: the unaligned sequences were aligned and sequences that only differed by gaps were identified. Only the longest of these were retained. This zip has the resulting alignment and lists of removed sequences. The python function trim_shorts_hamming() was used, which can be found here: https://github.com/bliebeskind/Alignment/blob/master/Alignment.py Trim2.zip: after removing these sequences, the data seq was realigned and trimmed of columns that were majority gapped. This zip has the trimmed alignments and the removed columns. Filtered_alignment: these trimmed alignments were then used to identify sequences that had fewer than 150 aligned residues, which were removed. This zip has the resultant alignments and lists of removed sequences. Trim3_final_alignment: This dataset was then realigned and trimmed of majority gapped columns to produce the final alignments used for Phylogenetic analysis. RawOutput: ConsensusTrees and MLTrees: Inferred from the final alignment using RAxML with the LG+CAT+F model and rapid bootstrap + ML search algorithm (-f a). The pThreading version of RAxML was run on the Lonestar nodes of the supercomputer TACC. The command was: raxmlHPC-PTHREADS-SSE3 -T 12 -f a -x 1235 -N 100 \ -m PROTCATLGF -s $INFILE -n $JOBNAME EvolMap_ancestor_results: The raw output of EvolMap for each gene for the combined data set. Notung_ConTree_infoFiles and Notung_MLTrees_infoFiles: The raw output of Notung when consensus trees and ML trees were used as input. AncestorAnalysis: EvolMap analysis: The parsed output from EvolMap, along with the labelled trees and other files used to run the PCA. The scripts used to parse the EvolMap and Notung output (below) can be found here: https://github.com/bliebeskind/AncestralGeneContent If you use this program, please cite the paper (thanks!) Notung_contree_analysis and Notung_MLTree_analysis: The parsed output from Notung, along with the all the files to run the PCA. FigS10: The alignment (MCMC setttings at the bottom of the nexus alignment file) and consensus tree used for FigS10.