grpPhylogeo: Determine sets of sequence presenting phylogeography signal
Description
From an alignment of sequence (fasta format) and a csv file with colomns nom (name of the sequence), lon and lat (GPS coordinates in degree.decimals of the longitude and latitude of sampling of the sequence), the function define sets of sequence presenting phylogeography signal using a mantel test between physic and genetic distance matrices.
Usage
grpPhylogeo(gbinfo, align, seuil = 0.1, method = "single",
model = "raw", pairwise.deletion=TRUE)
Arguments
gbinfo
name/path of a csv file with information on name (nom colomn) and GPS coordiantes of the sequence (lon and lat colomns)
align
sequence alignment in fasta format with the same name as those specified in the gbinfo file
seuil
significativity threshold for the mantel test
method
clustering method used; set to "single" by default; See the hclust function for details
model
DNA evolutionnary model use to compute genetic distance. Set to "raw" by default; See dist.dna (ape package) for details
pairwise.deletion
See dist.dna (ape package) for details
Value
A list of group of sequences with significative correlation between physic and genetic distance is returned.
Details
The function draw a clustering plot (with physic distance represented) with a red frame arround sequences with significative mantel test for correlation between physic and genetic distance.