Bayesian random local clocks, or one rate to rule them all
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:10.1186/1741-7007-8-114Published: 31 August 2010
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
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
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