AP_DRYAD

This contains input and output files generated using BEAST, *BEAST, and MrBayes. "*BEAST Calibration" contains XML files, log files, and species tree posterior distributions generated using a calibrated root for Ambystoma. "*BEAST MCC Trees" contains all MCC trees generated for all non-calibrated analyses using *BEAST. "*BEAST nexus and XML files" contains all XML files and nexus files associated with all non-calibrated analyses using *BEAST. "BEAST (for STEM) XML files" contains the XML files used for tree reconstruction of each locus using BEAST for downstream use in STEM. "BEAST MCC Trees (for STEM)" contains all MCC trees generated in BEAST for downstream use in STEM. "MrBayes Consensus Trees" contains all consensus trees generated using MrBayes. "MrBayes nexus Files" contains all nexus files used for analyses in MrBayes.