HCV Database
HCV sequence database
 



To our users Please note that the HCV database site is no longer funded. We try to keep the database updated and the tools running, but unfortunately, we cannot guarantee we can provide help for using this site. Data won't be manually curated either.


FindModel

Purpose: FindModel analyzes your alignment to see which phylogenetic model best describes your data; this model can then be used to generate a better tree.

File size limits: Finding the best evolutionary model is computationally intensive, so we limit default runs to a reduced set of 12 models, excluding those that do not have an obvious biological interpretation. (If you know of any system where Modeltest consistently returns a model that we do not include, please let us know.) The full set of 28 models can be run by checking the checkbox. Currently, input files smaller than 6 Kb for the reduced set and 3 Kb for the full set are run immediately; if your input file exceeds the limit, your job will be run in batch, and you will receive an e-mail with a link to your results. Currently, input files larger than 500 Kb for the reduced set and 350 Kb for the full set are too large for our machine to process.

Formats: FindModel only accepts aligned nucleotide input. The program attempts to automatically recognize the format of your input file. See below for troubleshooting tips.

Input
Paste your input here
or upload your file

Options
Use all 28 models
Construct initial tree using Weighbor
PAUP*
MrBayes
Always e-mail results



Troubleshooting: if you receive an error message, or no results within 24 hours, please consider the following.

If none of these problems is present, please contact us for additional help.


Background: FindModel was developed from a web implementation of the Modeltest script written by David Posada and Keith Crandall. It uses Bill Bruno's program Weighbor to generate the tree based on Jukes-Cantor distances. Weighbor is used because it is much faster than maximum likelihood, but less biased and more robust than NJ. Ziheng Yang's PAML is used to calculate the likelihood. The method from David Posada and Keith Crandall's MODELTEST paper is used to calculate AIC scores. One difference to the Modeltest evaluation is that we do not allow invariant sites, as this feature is not implemented in PAML because estimates of the fraction of invariant sites tend to be very sensitive to the number or taxa. NOTE: There is a downloadable interface for the original Modeltest code available from Genedrift.org; thanks to Stuart Ray for this information.

For background information on selecting evolutionary models, see (for example):

Johan Nylander has written an implementation of Modeltest that is based on MrBayes rather than PAUP.

More information: the functionality, methods, phylogenetic packages used, and the performance of this tool are presented in further detail in FindModel Info [PDF].

Contributors and References: Contributors to this implementation of FindModel include Ning Tao, Russell Richardson, William Bruno and Carla Kuiken.

 




Questions or comments? Contact us at hcv-info@lanl.gov