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 trimming
the tree to the ancestor node of tips in each group and then find
the bifurcated terminals of the trimmed tree. The nodepath
between root node and the bifurcated terminals is the lineages.
In order to extend the search of mutational site. The lineages
will tag some of its trailing nodes. Here nodes up to
the ancestor of the tips with the longest nodepath
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. If not provided, an average value of similarity among all sequences will be used. |
simMatrix |
S diagonal matrix of similarity between sequences |
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, 0.996)