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Table 1 The effects of a small subtype size

From: A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection

Subtype Nucleotide Frequency Probability
  A 89 99.83%
A C 0 0.06%
  G 0 0.06%
  T 0 0.06%
  A 392 99.71%
C C 1 0.27%
  G 0 0.01%
  T 0 0.01%
  A 2 93.18%
K C 0 2.27%
  G 0 2.27%
  T 0 2.27%
  1. Nucleotide frequencies and the derived emission probabilities for one column in an alignment of HIV-1 Group M sequences without using an information sharing protocol. The emission probabilities are estimated from the nucleotide frequencies using the pseudocounts α =(0.05, 0.05, 0.05, 0.05). We here restrict ourselves to 3 subtypes, A, C, and K.