treemer {sitePath} | R Documentation |
groupTips
uses sequence similarity to group tree tips.
Members in a group are always constrained to share the same
ancestral node. Similarity between two tips is derived from
their multiple sequence alignment. The site will not be counted
into total length if both are gap. Similarity is calculated
as number of matched divided by the corrected total length.
So far the detection of divergence is based on one simple rule:
the miminal pairwise similarity. The two branches are decided to
be divergent if the similarity is lower than the threshold.
(Other more statistical approaches such as Kolmogorov-Smirnov
Tests among pair-wise distance could be introduced in the future)
lineagePath
finds the lineages of a phylogenetic tree providing
the corresponding sequence alignment. This is done by finding 'major SNPs'
which usually accumulate along the evolutionary pathways.
are added.
groupTips( tree, similarity = NULL, simMatrix = NULL, forbidTrivial = TRUE, tipnames = TRUE ) lineagePath(tree, similarity = NULL, simMatrix = NULL, forbidTrivial = TRUE)
tree |
The return from |
similarity |
Similarity threshold for tree trimming in |
simMatrix |
A diagonal matrix of similarities for each pair of sequences. This parameter
will not have effect in the function |
forbidTrivial |
Does not allow trivial trimming |
tipnames |
If return as tipnames |
grouping of tips
path represent by node number
data('zikv_tree') data('zikv_align') tree <- addMSA(zikv_tree, alignment = zikv_align) groupTips(tree, 0.996) lineagePath(tree)