SPMM specifications

Unique identifier:
OMICS_13533
Interface:
Web user interface
Input data:
Aligned HIV envelope gene DNA sequences (either full length or a segment) obtained from one infected individual
Output data:
The pairwise Hamming distance distribution of the input HIV envelope gene sequences (grey box) along with the best fit of SPMM (red line), the fitted model parameters, days since infection, the number of founder variants, Hamming distances among founder sequences, the number of sequences in each founder lineage, and the Poisson parameter (λ), along with the goodness of fit p-value, the Sum of Squared Errors (SSE) and Akaike Information Criteria (AIC)
Computer skills:
Basic
Maintained:
Yes
Name:
Shifted Poisson Mixture Model
Restrictions to use:
None
Input format:
FASTA
Output format:
HTML
Stability:
Stable
  • Viruses
    • Human immunodeficiency virus

SPMM support

Maintainer

  • Ha Youn Lee <>

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Publications

Institution(s)

Department of Biostatistics and Computational Biology, University of Rochester, Chinahester, NY, USA; Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA; Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA

Funding source(s)

This work has been supported by NIH grants R01-AI083115 and R01- AI095066. Portions of this work were done under the auspices of the US Department of Energy under contract DE-AC52-06NA25396 and supported by NIH grants R01-AI028433, R01-OD011095 and UM1-AI100645.

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