Data from: A critical appraisal of the placement of Xiphosura (Chelicerata) with account of known sources of phylogenetic error

Ballesteros J, Sharma P

Date Published: February 12, 2019

DOI: https://doi.org/10.5061/dryad.2g1f4n5

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Title Concateneated dataset 3534 loci
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Description Primary dataset composed of 3534 loci concateneated. This file in combination with the all_stats.xls and the corresponding partition file can be used to produce all data subsets described in the manuscript.
Download Concat_3534_indep.fasta (78.66 Mb)
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Title Partition file of the 3534 loci dataset
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Download Partition_3534.txt.best_scheme.nex (228.2 Kb)
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Title MARE reduced dataset with 721 loci
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Download Concat_721_MARE.fasta (9.549 Mb)
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Title partition file MARE
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Download MAREpart.nex (40.70 Kb)
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Title functions for gene tree simulations
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Title mpsi
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Description Script for calculating mean pair-wise sequences identity metric
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Title droptips
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Description Script to prune a reference tree (species tree) from leaves not present in a given alignment. The script is used as a preliminary for Dellta GLS calculations.
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Title splitDist
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Description Script and functions to list and count the bipartitions present in a collection of trees.
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Title matrices.xlxs
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Description Spreadsheet listing all partitions, general properties, amino acid substitution models and results of Delta GLS and TtreSpEx LB scores. This file can also be used to filter dataset and reproduce the matrices in the manuscript.
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Title Supplemental_Tables_and_Figures
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Description Suplemental Tables and Figures including full annotated trees
Download Supplemental_Tables_and_Figures.pdf (23.95 Mb)
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Title datbacoca_pca
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Description Modified BaCoCa output used for PCA analyses.
Download datbacoca_pca.csv (1.738 Mb)
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Title part_1499
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Description Nexus file defining partitions and amino acid substitution models for the decisive dataset
Download part_1499.nex (85.38 Kb)
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Title NEWICKS 2
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Description Newick formatted trees.
Download NEWICKS 2.zip (112.5 Kb)
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Title Pycnogonium_littorale_SAMN10093767
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Description Transcriptome assembly
Download Pycnogonium_littorale_SAMN10093767.fasta (47.22 Mb)
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Title Lithobius_atkinsoni_SAMN10093766
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Download Lithobius_atkinsoni_SAMN10093766.fasta (568.2 Mb)
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When using this data, please cite the original publication:

Ballesteros JA, Sharma PP (2019) A Critical Appraisal of the Placement of Xiphosura (Chelicerata) with Account of Known Sources of Phylogenetic Error. Systematic Biology, online in advance of print. https://doi.org/10.1093/sysbio/syz011

Additionally, please cite the Dryad data package:

Ballesteros J, Sharma P (2019) Data from: A critical appraisal of the placement of Xiphosura (Chelicerata) with account of known sources of phylogenetic error. Dryad Digital Repository. https://doi.org/10.5061/dryad.2g1f4n5
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