readTrees | R Documentation |
reads trees from a 2 column , tab seperated, file The first columns is the gene name and the second column is the corresponding tree in parenthetic format known as the Newick or New Hampshire format
readTrees(
file,
max.read = NA,
masterTree = NULL,
minTreesAll = 20,
reestimateBranches = F,
minSpecs = NULL
)
file |
The path to the tree file |
max.read |
This function takes a while for a whole genome, so max.read is useful for testing |
masterTree |
(optional) User can specify a master tree. Recommended only when the number of available gene trees with all species is small. |
minTreesAll |
The minimum number of trees with all species present in order to estimate master tree edge lengths (default 20). |
reestimateBranches |
Boolean indicating whether to re-estimate branch lengths if master tree topology is included (default FALSE) |
minSpecs |
the minimum number of species that needs to be present in a gene tree to be included in calculating master tree |
A trees object of class "treeObj"
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