Build a phylogenetic tree

buildSeqTree(
  x,
  pml_model = "GTR",
  pml_optInv = TRUE,
  pml_optGamma = TRUE,
  pml_rearrangement = "stochastic",
  pml_control = pml.control(trace = 0)
)

Arguments

x: Sequences DNAStringSet
pml_model: See optim.pml phangorn
pml_optInv: See optim.pml phangorn
pml_optGamma: See optim.pml phangorn
pml_rearrangement: See optim.pml phangorn #'
pml_control: See optim.pml phangorn

Details

A wrapper to build phylogenetic tree for ASV sequences obtained after dada2.

Examples

library(biomeUtils)
data("SprockettTHData")
# select few for example
seqs <- sample(SprockettTHData@refseq, 5)
sp.tree <- buildSeqTree(seqs)
#> Determining distance matrix based on shared 8-mers:
#> ================================================================================
#> 
#> Time difference of 0 secs
#> 
#> Clustering into groups by similarity:
#> ================================================================================
#> 
#> Time difference of 0 secs
#> 
#> Aligning Sequences:
#> ================================================================================
#> 
#> Time difference of 0.03 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 0.02 secs
#> 
#> Alignment converged - skipping remaining iteration.
#> 
sp.tree$tree
#> 
#> Phylogenetic tree with 5 tips and 3 internal nodes.
#> 
#> Tip labels:
#>   ASV_4310_Actinomyces_bowdenii, ASV_6427_Fusobacterium_varium, ASV_1399_Christensenellaceae_R-7_group, ASV_5156_Cloacibacillus_evryensis, ASV_6471_Leptotrichia
#> 
#> Unrooted; includes branch lengths.