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%

 Nucleotide frequencies and the derived emission probabilities for one column in an alignment of HIV1 Group M sequences without using an information sharing protocol. The emission probabilities are estimated from the nucleotide frequencies using the pseudocounts $\overrightarrow{\alpha}=\left(\text{0.05, 0.05, 0.05, 0.05}\right)$. We here restrict ourselves to 3 subtypes, A, C, and K.