Major revisions in pancrustacean phylogeny and evidence of sensitivity to taxon sampling
Data files
Nov 17, 2022 version files 21.71 MB
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divergence_time_files.zip
38.27 KB
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matrices.zip
16.21 MB
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orthologs.zip
5.41 MB
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README.md
4.63 KB
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treefiles.zip
40.20 KB
Mar 20, 2023 version files 24.99 MB
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divergence_time_files.zip
38.27 KB
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matrices.zip
19.45 MB
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orthologs.zip
5.41 MB
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README.md
6.54 KB
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treefiles.zip
81.90 KB
Apr 05, 2023 version files 223.50 MB
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Dataset2_homologs.tar.gz
198.51 MB
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divergence_time_files.zip
38.27 KB
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matrices.zip
19.45 MB
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orthologs.zip
5.41 MB
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README.md
6.74 KB
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treefiles.zip
81.90 KB
Apr 04, 2023 version files 234.60 MB
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Dataset2_homologs.tar.gz
198.51 MB
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divergence_time_files.zip
38.27 KB
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matrices.zip
19.45 MB
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orthologs.zip
16.52 MB
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README.md
7.41 KB
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treefiles.zip
81.90 KB
Abstract
Matricies, treefiles, and alignments from: Major revisions in pancrustacean phylogeny and evidence of sensitivity to taxon sampling
Description of the data and file structure
zip files for:
- divergence_time_files # chronograms from divergence time analyses
- matrices # super matrices (full alignments) used in this study
- orthologs # individual ortholog alignments and gene trees
- treefiles # newick tree files (filenames refer to the figure numbers in the manuscript)
- Dataset2_homologs # unaligned fastas before ortholog filters
Detailed Table of Contents
- divergence_time_files
- dating_MCMCTree_c1.chronogram # chronogram from chain 1 of MCMCTree divergence time analsis
- dating_MCMCTree_c3.chronogram # chronogram from chain 2 of MCMCTree divergence time analsis
- dating_MCMCTree_c2.chronogram # chronogram from chain 3 of MCMCTree divergence time analsis
- dating_MCMCTree_prior.chronogram # chronogram under the prior of MCMCTree divergence time analsis
- Phylobayes_LN.chronogram # chronogram of 3 chains using the LN model in Phylobayes
- Phylobayes_LN_prior.chronogram # chronogram of 3 chains under the prior of the LN model in Phylobayes
- Phylobayes_CIR.chronogram # chronogram of 3 chains using the CIR model in Phylobayes
- Phylobayes_CIR_prior.chronogram # chronogram of 3 chains under the prior of the CIR model in Phylobayes
- Phylobayes_UGAM.chronogram # chronogram of 3 chains using the UGAM model in Phylobayes
- Phylobayes_UGAM_prior.chronogram # chronogram of 3 chains using the UGAM model in Phylobayes
- matrices
- Dataset1_matrix.phy # Dataset 1 is an earlier version of this study containing 98 taxa and 559 orthologs (details in manuscript text)
- Dataset1_shared_orthologs_only_alignment.fasta # Matrix of the 98 taxa in Dataset 1 with only the 267 orthologs shared with Dataset 2
- Dataset2_matrix.phy # Final matrix consisting of 105 taxa (details in manuscript text)
- Dataset2_50gene_subset_Phylobayes_divergence.phy # Matrix of top 50 genes from Dataset 2 with highest Robinson-Foulds similarity to species tree from ML analysis of Dataset2_matrix.phy
- Dataset2_matrix_dayhoff_recoded.phy # Dataset 2 matrix under Dayhoff6 recoding
- Dataset2_minus_fastestgenes_matrix.phy # Dataset 2 with the 10% (i.e., 57) fastest evolving genes removed
- Dataset2_shared_orthologs_only_alignment.fasta # Matrix of the 105 taxa in Dataset 2 with only the 267 orthologs shared with Dataset 1
- Dataset2_matrix_trimmed_of_added_taxa.fasta # Taxon sampling experiment. Dataset 2 matrix after removing the additional taxa that were added relative to Dataset 1 (details in manuscript text)
- orthologs
- Dataset1_ortholog_alignments_gblocks.zip # individual alignments for the 559 orthologs in Dataset 1
- Dataset1_ortholog_alignments.tar.gz # individual alignments for the 559 orthologs in Dataset 1 prior to trimming with gblocks
- Dataset1_ortholog_trees.zip # individual gene trees for the 559 orthologs in Dataset 1
- Dataset2_ortholog_alignments_gblocks.zip # individual alignments for the 576 orthologs in Dataset 2
- Dataset2_ortholog_alignments.tar.gz # individual alignments for the 576 orthologs in Dataset 2 prior to trimming with gblocks
- Dataset2_ortholog_trees.zip # individual gene trees for the 576 orthologs in Dataset 2
- Datatset3_vs_Dataset1_shared_orthologs.txt # list of orthologs shared between Datasets 2 and 3
- treefiles
- Fig2A_Dataset2_C60LG.tre # Tree resulting from LG+C60+F+G analysis of Dataset 2 AA matrix
- FigS1A_Dataset2_raxml.tre # Tree resulting from RAxML analysis of Dataset 2 AA matrix
- FigS1B_Dataset2_Dayhoff6_raxml.tre # Tree resulting from RAxML analysis of Dataset 2 Dayhoff6 matrix
- FigS1C_Dataset2_C60LG_minusfastgenes.tre # Tree resulting from IQ-TREE LG+C60+F+G analysis of Dataset 2 AA matrix with 10% fastest evolving genes removed
- FigS2A_Dataset2_CATGTR_consensus.tre # Tree resulting from Phylobayes CAT-GTR analysis of Dataset 2 AA matrix - consensus of 3 chains
- FigS2B_Dataset2_CATGTR_c1.tre # Tree resulting from Phylobayes CAT-GTR analysis of Dataset 2 AA matrix - chain 1
- FigS2C_Dataset2_CATGTR_c2.tre # Tree resulting from Phylobayes CAT-GTR analysis of Dataset 2 AA matrix - chain 2
- FigS2D_Dataset2_CATGTR_c3.tre # Tree resulting from Phylobayes CAT-GTR analysis of Dataset 2 AA matrix - chain 3
- FigS3_Dataset2_Dayhoff6_CATGTR_consensus.tre # Tree resulting from Phylobayes CAT-GTR analysis of Dataset 2 Dayhoff6 matrix - consensus of 2 chains
- FigS4A_Dataset2_ATRAL.tre # Tree resulting from ASTRAL analysis of Dataset 2 orthologs
- FigS4B_Dataset2_ASTRAL_BS10.tre # Tree resulting from ASTRAL analysis of Dataset 2 orthologs, with nodes in gene trees with <10% BS support collapsed
- FigS4C_Dataset2_ASTRAL_BS20.tre # Tree resulting from ASTRAL analysis of Dataset 2 orthologs, with nodes in gene trees with <20% BS support collapsed
- FigS4D_Dataset2_ASTRAL_BS30.tre # Tree resulting from ASTRAL analysis of Dataset 2 orthologs, with nodes in gene trees with <30% BS support collapsed
- FigS5_Dataset1_C60LG_speciestree.treefile # Tree resulting from LG+C60+F+G analysis of Dataset 1 AA matrix
- FigS6_Dataset1_Dayhoff6_raxml.tre # Tree resulting from RAxML analysis of Dataset 1 Dayhoff6 matrix
- FigS7_Dataset1_CATGTR_consensus.tre # Tree resulting from Phylobayes CAT-GTR analysis of Dataset 1 AA matrix - consensus of 4 chains
- FigS8A_Dataset1_Dayhoff6_CATGTR_consensus.tre # Tree resulting from Phylobayes CAT-GTR analysis of Dataset 1 Dayhoff6 matrix - consensus of 2 chains
- FigS8B_Dataset1_Dayhoff6_CATGTR_c1.tre # Tree resulting from Phylobayes CAT-GTR analysis of Dataset 1 Dayhoff6 matrix - chain 1
- FigS8C_Dataset1_Dayhoff6_CATGTR_c2.tre # Tree resulting from Phylobayes CAT-GTR analysis of Dataset 1 Dayhoff6 matrix - chain 2
- FigS9A_Dataset1_ASTRAL.tre # Tree resulting from ASTRAL analysis of Dataset 1 orthologs
- FigS9B_Dataset1_ASTRAL_BS10.tre # Tree resulting from ASTRAL analysis of Dataset 1 orthologs, with nodes in gene trees with <10% BS support collapsed
- FigS9C_Dataset1_ASTRAL_BS30.tre # Tree resulting from ASTRAL analysis of Dataset 1 orthologs, with nodes in gene trees with <30% BS support collapsed
- FigS10A_Dataset1_shared_orthologs_C60LG.tre # Trees results from IQ-TREE LG+C60+F+G analysis using only shared orthologs - Dataset 1 taxa
- FigS10B_Dataset2_shared_orthologs_C60LG.tre # Trees results from IQ-TREE LG+C60+F+G analysis using only shared orthologs - Dataset 2 taxa
- FigS11_Dataset2_C60LG_trimmed_taxa.tre # Trees resulting from LG+C60+F+G analysis of the Dataset 2 orthologs trimmed of additional taxa relative to Dataset 1
- Dataset2_homologs.tar.gz # unaligned fastas before ortholog filters. Results from all vs all BLAST and MCL, clusters with >40 taxa
Phylogenetic trees and alignments from analyses in this study.