search for: phylogram

Dear all, I'd like to introduce a new R package called *phylogram,* for working with evolutionary trees as deeply-nested lists known as "dendrogram" objects. The package provides functions for importing and exporting phylogenetic trees in the Newick parenthetic text format, as well as several functions for command-line tree manipulation. With an empha...

...rongly ordered and don't correspond to the Rowv dendrogram. I know there is a bug with the heatmap fonction. Emmanuel Paradis (http://tolstoy.newcastle.edu.au/R/e2/help/07/05/16227.html )suggested a modification to fix it but in my case the row labels are still wrongly ordered. Heatmaps with 2 phylograms have been published in different papers, so a solution exists to fix this bug. Could anyone help me ? [[alternative HTML version deleted]]

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attemptin...

Hi, I've been investigating the ape package for a while, and I was wondering if it is possible to: - display the names of the internal nodes (from a newick tree) - plot a pie-chart on top of each of the internal branches in a phylogram plot Thanks in advance, Cheers, Albert.

...the forward, backward & Viterbi algorithms. The package has a wide variety of uses including database searching, gene-finding and annotation, phylogenetic analysis and sequence classification. The number of dependencies has been kept to a minimum (non-base dependencies: Rcpp, openssl & phylogram), and while aphid is designed to be used in conjunction with the ?ape? package, it is not a requisite. Indeed, the package functions will work with any standard character sequence vectors (even non-biological ones), though at a cost of memory efficiency when compared with ape?s raw DNAbin and AAbin...

Hi, I'm doing hierarchical clustering, and want to export my dendrogram to a tree-viewing/editing software. I can do this by converting the data to Newick format (hc2Newick in ctc package), but I can't get branch lengths to show in the resulting phylogram. I figured it might help to convert my hclust object into a phylo object (as.phylo in ape package), but the following lines give me this "Error in UseMethod("as.phylo") : no applicable method for 'as.phylo' applied to an object of class "character": data = read.tab...

...the forward, backward & Viterbi algorithms. The package has a wide variety of uses including database searching, gene-finding and annotation, phylogenetic analysis and sequence classification. The number of dependencies has been kept to a minimum (non-base dependencies: Rcpp, openssl & phylogram), and while aphid is designed to be used in conjunction with the ?ape? package, it is not a requisite. Indeed, the package functions will work with any standard character sequence vectors (even non-biological ones), though at a cost of memory efficiency when compared with ape?s raw DNAbin and AAbin...