Poisson-Fitter

Purpose: Poisson-Fitter analyzes sets of homogeneous DNA sequences and performs statistical tests on the Hamming Distance frequency distributions. It computes the best fitting Poisson distribution through Maximum Likelihood, performs a Goodness of Fit test, and tests for Star-Phylogeny.

Details: The tool accepts a single input file, which may contain sets of aligned sequences from one or more patients. The alignments can be in any one of the Common Sequence Formats. We recommend that all sequences in each intrapatient set should start and end at the same position. Each intrapatient alignment must begin with a consensus sequence, named as shown in this example:
>XXXX.CONSENSUS
where XXXX is the name of the sample. For complete details, see Poisson Fitter Explanation, where we also explain how to make a consensus sequence if you don't have one.

Reference: Please reference this article when using Poisson Fitter:

• Giorgi EE, Funkhouser B, Athreya G, Perelson AS, Korber BT, Bhattacharya T. Estimating time since infection in early homogeneous HIV-1 samples using a Poisson model. BMC Bioinformatics 2010 Oct 25;11:532. PMID: 20973976