# get.entropy: Compute the Sequence Entropy for an Alignment In BioPhysConnectoR: BioPhysConnectoR

## Description

Computes the sequence entropy of an alignment. It is possible to specify which characters to omit in the computation. The joint entropy is computed using `get.entropy2p()`.

## Usage

 ```1 2 3 4 5``` ```get.entropy(aln, bool = FALSE, gapchar = "NOGAPCHAR", verbose = FALSE) get.entropy2p(aln, bool = FALSE, gapchar = "NOGAPCHAR", verbose = FALSE) ```

## Arguments

 `aln` alignment matrix `bool` logical, if TRUE gaps are ignored when computing the entropy of each column of the alignment `gapchar` character vector containing the unique set of characters representing gaps in the amino acid sequence `verbose` logical, TRUE for getting output messages

## Details

The Shannon (1948) entropy for an alignment is computed as follows:

H(X)=-sum_x p(x)log_2(p(x))

The joint entropy is computed for every possible column pair:

H(X)=-sum_(x,y) p(x,y)log_2(p(x,y))

where X and Y are two columns of the alignment.

## Value

Return value for `get.entropy()` is a vector containing the entropy for each column.
Return value for `get.entropy2p()` is a matrix containing the joint entropies in the lower triangle.

## Author(s)

Franziska Hoffgaard

## References

Shannon (1948) The Bell System Technical Journal 27, 379–423.

`get.mie`
 ```1 2 3 4 5 6``` ```aln<-matrix(c("M", "H", "X", "P", "V", "-", "H", "X", "L", "V", "M", "L", "X", "P", "V"), 3, byrow = TRUE) h1<-get.entropy(aln, bool = TRUE , gapchar = "-") h2<-get.entropy(aln) h3<-get.entropy2p(aln) ```