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()`

.

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

`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 |

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.

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.

Franziska Hoffgaard

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)
``` |

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