mat.dif {bios2mds} | R Documentation |

## Matrices of difference scores between sequences

### Description

Computes a matrix providing the distances based on the difference scores between sequences from two multiple sequence alignments.

### Usage

```
mat.dif(align1, align2, gap = FALSE, aa.strict = FALSE, sqrt = FALSE)
```

### Arguments

`align1` |
a list of character vectors representing a first multiple sequence aligment. |

`align2` |
a list of character vectors representing a second multiple sequence aligment. |

`gap` |
a logical value indicating whether gap character should be taken as supplementary symbol (TRUE) or not (FALSE). Default is FALSE. |

`aa.strict` |
a logical value indicating whether only strict amino acids should be taken into account (TRUE) or not (FALSE). To be used only for amino acid sequences. Default is FALSE. |

`sqrt` |
a logical value indicating whether the distance should be equal to the squared root of the difference score (TRUE) or not (FALSE). Default is FALSE. |

### Details

If `align1`

and `align2`

are identical, `mat.dif`

computes the symetrical matrix of distances between each sequence of the alignment.

Before using `mat.dif`

, users must check the alignment of sequences within `align1`

and `align2`

and between `align1`

and `align2`

.

### Value

A named numeric matrix providing the difference-based distances between each pair of sequences from `align1`

and `align2`

. The number of rows and columns is identical to the number of sequences in `align1`

and `align2`

, respectively.

### Author(s)

Julien Pele and Jean-Michel Becu

### See Also

`identity`

function from `bio3d`

package.

### Examples

```
# calculating the matrix of distances based on the difference scores
# between GPCRs sample from H. sapiens and D. melanogaster:
aln_human <- import.fasta(system.file("msa/human_gpcr.fa", package = "bios2mds"))
aln_drome <- import.fasta(system.file("msa/drome_gpcr.fa", package = "bios2mds"))
mat.dif1 <- mat.dif(aln_human[1:5], aln_drome[1:5])
mat.dif1
```

*bios2mds*version 1.2.3 Index]