TreeRate beta

Troubleshooting

• Does your Newick file contain internal node names? Trees generated by certain tools contain internal node names. This beta version cannot interpret these. Remove the internal node names, or generate a new tree file that does not contain them. See TreeRate Explanation.
• Are your branchlengths expressed as exponents? Trees generated by certain tools have branchlengths expressed as exponents. This beta version cannot interpret these and will be unable to parse your tree. Please change these values to decimals, or generate a new tree file that uses decimals.
• Error message: "Duplicate taxa". A common reason for this error is the presence of internal node names. See TreeRate Explanation. This error can also occur if you have duplicated names, or if your taxa names are so long that they are truncated by the tool.
• Other problems? This is the beta version of TreeRate, so please send us an e-mail if you have problems that cannot be solved by these tips. For faster help, please send us your input file. Thank you for your understanding.

References

Please reference these articles when using TreeRate:

• Maljkovic Berry I, Ribeiro R, Kothari M, Athreya G, Daniels M, Lee HY, Bruno W, Leitner T. Unequal Evolutionary Rates in the Human Immunodeficiency Virus Type 1 (HIV-1) Pandemic: the Evolutionary Rate of HIV-1 Slows Down When the Epidemic Rate Increases. 2007 J Virol 81:10625-10635.
• Maljkovic Berry I, Athreya G, Kothari M, Daniels M, Bruno W, Korber B, Kuiken C, Ribeiro R, Leitner T. A simple method for optimizing the root in phylogenetic trees with longitudinal data reveals an evolutionary rate that tracks the epidemiological dynamics of HIV-1. 2009 Epidemics 1(4): 230-239.