HyRAD-X exome capture museomics unfolds giant ground beetle evolution

This dataset contains all final files from the study entitled "HyRAD-X exome capture museomics unfolds giant ground beetle evolution" and published in Genome Biology and Evolution. To access the raw data of the HyRAD-X project please go to the SRA database and look for the BioProject ID PRJNA706141.

Phylogenomic Datasets and partitioning schemes used in the study:

A_2945_BWA_MEM_loci_43_Taxa.phy / HyRAD-X Dataset A       
A_2945_BWA_MEM_loci_partition.nex / Partitioning scheme for Dataset A
B_2945_BWA_MEM_loci_40_Taxa.phy / HyRAD-X Dataset B        
C_1227_BWA_ALN_loci_40_Taxa.phy / Partitioning scheme for Dataset B       
C_1227_BWA_ALN_loci_partition.nex / HyRAD-X Dataset C       
D_100_BWA_MEM_loci_43_Taxa.phy / HyRAD-X Dataset D        
D_100_BWA_MEM_loci_partition.nex /  Partitioning scheme for Dataset D        
E_MtGenomes_60_Taxa.phy / Mitogenomic Dataset E       
E_MtGenomes_partition.nex / Partitioning scheme for Dataset E  

Divergence time estimation datasets used in the study:     

HyRAD-X_BEAST_100loci_SortaDate.nex / Input alignment for BEAST analysis based on SortaDate selection        
HyRAD-X_BEAST_100loci_SortaDate_BD_1C_2F2SC_40TAX.xml / XML input file for BEAST        
HyRAD-X_BEAST_100loci_SortaDate_BD_7C_2F2SC_40TAX.xml / XML input file for BEAST         
HyRAD-X_BEAST_100loci_SortaDate_Yule_1C_2F2SC_40TAX.xml / XML input file for BEAST         
HyRAD-X_BEAST_100loci_SortaDate_Yule_7C_2F2SC_40TAX.xml / XML input file for BEAST         

Final tree files used in the study:     

ML Phylogeny Dataset A BWA MEM 43 Taxa.tre / .tre file from best scoring IQ-TREE ML search using Dataset A     
ML Phylogeny Dataset B BWA MEM 40 Taxa.tre / .tre file from best scoring IQ-TREE ML search using Dataset B         
ML Phylogeny Dataset C BWA ALN 40 Taxa.tre / .tre file from best scoring IQ-TREE ML search using Dataset C         
ML Phylogeny Dataset D BWA MEM SortaDate 43 Taxa.tre / .tre file from best scoring IQ-TREE ML search using Dataset D 
ML Phylogeny Dataset E Mitogenomes.tre / .tre file from best scoring IQ-TREE ML search using Dataset E         
Bayesian BEAST MCC Tree Yule 7C.tre / .tre file from best scoring BEAST analysis 

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