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Open Access Highly Accessed Research article

Bayesian random local clocks, or one rate to rule them all

Alexei J Drummond12 and Marc A Suchard34

Author Affiliations

1 Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Private Bag 92019, Auckland, New Zealand

2 Computational Evolution Group, University of Auckland, Private Bag 92019, Auckland, New Zealand

3 Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA

4 Department of Biostatistics, UCLA School of Public Health, Los Angeles, CA 90095, USA

BMC Biology 2010, 8:114  doi:10.1186/1741-7007-8-114

Published: 31 August 2010

Additional files

Additional file 1:

Supplementary Information. This is a PDF file describing some additional details of the described methods including (i) a description of the proposal distribution for trees used in the RLC model and (ii) a summary of the analysis of the influenza data using a "fixed epoch" model that allows the rate of evolution to change at a specific time in the past.

Format: PDF Size: 507KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Human.H3.81-98-local-gamma.xml. This is a BEAST XML input file compatible with BEAST 1.5.4 that implements the model combination used to analyze the influenza data set under the RLC model.

Format: XML Size: 86KB Download file

Open Data

Additional file 3:

Human.H3.81-98-2rate.xml. This is a BEAST XML input file compatible with BEAST 1.5.4 that implements the "fixed epoch" model used to confirm the signal for a temporal ate change in the influenza data set.

Format: XML Size: 88KB Download file

Open Data