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Scripts and simulated data associated with the manuscript "Reference genome choice and filtering thresholds jointly influence phylogenetic analyses". Scripts can also be found at https://github.com/jessicarick/refbias_scripts, but were archived here at the time of manuscript submission.

\n\n

 

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refbias_scripts-preprint.tar.gz contains scripts from GitHub repository

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simphy_trees.tar.gz contains simulated species trees

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sim_results_raxml_astral.tar.gz contains trees and tree statistics for simulation analyses

\n\n

emp_results_raxml_astral.tar.gz contains trees and tree statistics for empirical analyses

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simulation_vcfs.tar.gz contains filtered VCFs that were used for inferring phylogenies

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