plotEntropy: Plot the entropy profile for a matrix of sequences
In aramette/otu2ot: Calculate oligotypes for aligned FASTA sequences

Description Usage Arguments Value Author(s) Examples

Plot the entropy profile for a matrix of sequences and also the base composition for the positions with highest entropy values.

1	plotEntropy(Seqs,Legend=TRUE,Max=TRUE,EntropyThreshold=0.6)

`Seqs`	a matrix of bases (nt sites are the columns; rows as the individual sequences).
`Legend`	logical. if the plot has a legend or not.
`Max`	logical. if only the max entropy should be displayed.
`EntropyThreshold`	numeric. A fixed entropy threshold above which the positions are identified. Only considered if Max=FALSE

This function returns nothing, but prints the positions of the maximum entropy and the statistics (number and proportions for each different base at each position).

Alban Ramette

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data(mock.fasta)
plotEntropy(Seqs=mock.fasta[[2]],Legend = TRUE,Max=TRUE)
plotEntropy(Seqs=mock.fasta[[2]],Legend = TRUE,Max=FALSE,EntropyThreshold = 0.6)