Published June 5, 2023 | Version 1.1
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Parameter estimation and species tree rooting using ALE and GeneRax

  • 1. University of Bristol


Some output files associated with the analyses in an article (currently) entitled "Parameter estimation and species tree rooting using ALE and GeneRax"

The outputs were obtained by running ALEml_undated either with default (maximum likelihood) estimation of the delta, tau, and lambda parameters, or with delta:tau fixed to a pre-defined ratio. The option to fix delta:tau (or other parameter combinations) was recently added to ALE (

The .ale files used as input for these analyses (for the bacterial dataset) are available from the data repository for the original 2021 paper here:



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