Create a Phylogenetic Tree Object

Create a phylo tree object using a manipulated DNA string set object.

Usage

genPhytree(manipulated_stringset)

Arguments

manipulated_stringset

A manipulated string set object.

Value

A phylogenetic tree object

Examples

# create and plot a phylo tree

specdf_Anth <- querySpecData("Antheraea polyphemus")[1:10,]

DNABin_Anth <- genDNABin(specdf_Anth)

DNAStringset_Anth <- genDNAStringSet(DNABin_Anth)
#> Warning: cannot remove file 'new_DNAString_file.fasta', reason 'Permission denied'

DNAStringSet_Anth_manipulated <- ManipStringSet(DNAStringset_Anth)
#> ========================================================================================================================================================================================================
#> 
#> Time difference of 0.05 secs
#> Determining distance matrix based on shared 9-mers:
#> ================================================================================
#> 
#> Time difference of 0 secs
#> 
#> Clustering into groups by similarity:
#> ================================================================================
#> 
#> Time difference of 0 secs
#> 
#> Aligning Sequences:
#> ================================================================================
#> 
#> Time difference of 0.05 secs
#> 
#> Iteration 1 of 2:
#> 
#> Determining distance matrix based on alignment:
#> ================================================================================
#> 
#> Time difference of 0 secs
#> 
#> Reclustering into groups by similarity:
#> ================================================================================
#> 
#> Time difference of 0 secs
#> 
#> Realigning Sequences:
#> ================================================================================
#> 
#> Time difference of 0.05 secs
#> 
#> Alignment converged - skipping remaining iteration.
#> 

Phytree_Anth <- genPhytree(DNAStringSet_Anth_manipulated)

Phytree_Anth$edge.length <- Phytree_Anth$edge.length + (mean(Phytree_Anth$edge.length) * 0.1)

plot(Phytree_Anth)