User: Klaus S

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Klaus S140
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4 years, 7 months ago
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Posts by Klaus S

<prev • 5 results • page 1 of 1 • next >
2
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Answer: A: prunning posterior distribution of trees in R
... `keep.tip` from ape and `lapply` should do the job: library(ape) trees <- .uncompressTipLabel(trees) trees <- lapply(trees, keep.tip, trait_names) trees class(trees) <- "multiPhylo" trees <- .compressTipLabel(trees) Here `trees` is a `multiPhylo` object (you c ...
written 16 months ago by Klaus S140
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Answer: A: Calculate distance matrix from nucleotide alignment with multiple IUPAC ambiguit
... The function `dist.ml` in the R package phangorn handles ambiguity characters like they are handled in ML optimisation. library(phangorn) dat <- read.phyDat("msa.fas", format="fasta) dist.ml(dat, model = "F81", exclude = "none") ...
written 16 months ago by Klaus S140
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Answer: A: Adding branch lengths to a topology
... You can do it in R >library(phangorn) >dat <- read.phyDat("your_file.fas", format = "fasta") # read in data >ntip <- length(dat) >tree <- stree(ntip, tip.label = names(Laurasiatherian)) # create star tree >tree$edge.length <- rep(. ...
written 18 months ago by Klaus S140 • updated 17 months ago by genomax90k
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Answer: A: Phylogenetics in R: obtaining internal branch lengths
... If you would have looked in the help of `read.tree`, you will find: ... Value an object of class "phylo" with the following components: edge a two-column matrix of mode numeric where each row represents an edge of the tree; the nodes and the tips are symbolized with numbers; the tips are numb ...
written 4.4 years ago by Klaus S140
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Answer: A: R phangorn phylogenetic analysis from somatic mutations' binary table
... Hello Alejandro, There are generic functions `as.phyDat()` in phangorn to transform matrices and data.frames into phyDat objects. For example you can read in your data with `read.table()` or `read.csv()`, but you might need to transpose your data. For matrices `as.phyDat()` assumes that the entri ...
written 4.6 years ago by Klaus S140 • updated 2.0 years ago by RamRS30k

Latest awards to Klaus S

Scholar 17 months ago, created an answer that has been accepted. For A: R phangorn phylogenetic analysis from somatic mutations' binary table
Scholar 4.6 years ago, created an answer that has been accepted. For A: R phangorn phylogenetic analysis from somatic mutations' binary table
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: R phangorn phylogenetic analysis from somatic mutations' binary table

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