similar to: New package: phylogram

Hi folks, I'm pleased to introduce a new package called ?aphid?, for analysis with profile hidden Markov models in R. The package contains functions for multiple and pairwise sequence alignment for both nucleic acids and proteins (preferably in the DNAbin or AAbin format), model building, parameter optimization (Baum Welch and Viterbi training), plotting, file import & export,

Hi folks, I'm pleased to introduce a new package called ?aphid?, for analysis with profile hidden Markov models in R. The package contains functions for multiple and pairwise sequence alignment for both nucleic acids and proteins (preferably in the DNAbin or AAbin format), model building, parameter optimization (Baum Welch and Viterbi training), plotting, file import & export,

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 attempting to generate

Ape is an R package for "analyses of phylogenetics and evolution". The first version (0.1) has been released on 27 August 2002 and is available on CRAN. >From the 'Description' file of version 0.1: Ape provides functions for reading, and plotting phylogenetic trees in parenthetic format (standard Newick format), analyses of comparative data in a

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.

Dear R-helpers and Klaus, I would like to know how to write out a tree file with bootstrap from phangorn package. That tree file could be in newick format or others. I am new for phylogenetic operation in R. Could you please give me any directions on that? Thanks in advance. Best wishes, Jian-Feng, ######## # as a example # I accomplished 1000 bootstrap simulation on a fit object (a maximum

Dear all, The version 1.0 of ape (analysis of phylogenetics and evolution) is now on CRAN. The jump from version 0.2-1 to 1.0 is explained by the fact that the initial objectives of the project have been completed. The relevant part of the Changes file is shown below. All comments, suggestions, or bug reports are welcome. Emmanuel Paradis CHANGES IN APE VERSION 1.0 NEW FEATURES

Dear all, Does anyone know how can one loop through the newick phylogenetic trees stored in a nexus file and generate an "average" skyline plot with coalescent intervals? I have managed to generate the plot with one tree, but is it possible to create that "consensus/average" plot in R? tr<-"((((8.1:0, 20.1:0):0, 6.1:3):123, (((((35.1:0, (22.1:0, (43.1:1,

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

Hi, I have trouble with the heatmap function (package stats). The row labels are wrongly 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

Dear all, I am working with taxonomic data, represented as a list of classes, orders, families, genera and finally species. > class(mydata) [1] "data.frame" > mode(mydata) [1] "list" > names(mydata) [1] "tclass" "torder" "tfamily" "tgenus" "tspecies" > length(mydata$tclass) [1] 161590 The first 10

Dear R-helpers, I would like to export hierarchical clusters e.g. fit <- hclust(d, method="ward") in the newick format write(hc2Newick(fit),file='hclust.newick') Searching for a possibility I found this solution in the package ctc (http://www.bioconductor.org/packages/bioc/html/ctc.html). However, neither from this site nor via CRAN it is possible to install the package.

Hi R helpers... I am having troubles because of the discrepancy between the dendrogram plotted from hclust and what is wrote in the hc2Newick file. I've got a matrix C: > hc <- hclust(dist(C)) > plot(hc) with the: > write(hc2Newick(hc),file='test.newick') both things draw completely different "trees"... I have also tried with the raw distance matrix D and

Dear all, I wanted to let you know about four phylogenetic comparative methods (PCM) packages that have become available on (3 on CRAN and 1 on GitHub) recently that hopefully will be interesting to somebody. Three of them go significantly beyond the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes. 1) There is a new version of mvSLOUCH available. The most important change is that the

Dear all, I wanted to let you know about four phylogenetic comparative methods (PCM) packages that have become available on (3 on CRAN and 1 on GitHub) recently that hopefully will be interesting to somebody. Three of them go significantly beyond the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes. 1) There is a new version of mvSLOUCH available. The most important change is that the

CRAN (and crantastic) updates this week New packages ------------ * bdoc (1.0) Michael Anderson http://crantastic.org/packages/bdoc This package contains a function that will classify DNA barcodes as well as a few test and reference data sets. * bdsmatrix (1.0) Terry Therneau http://crantastic.org/packages/bdsmatrix This is a special case of sparse matrices, used by coxme and

POSITION SUMMARY Postdoctoral Research Fellow at EcoHealth Alliance, New York, to study the evolution and ecology of zoonotic diseases from bats and other hosts. PRIMARY RESPONSIBILITIES The position is funded by a National Institutes of Health NIAID award to discover, characterize, and model the risk of new potential zoonoses from bats. The primary focus of the Research Fellow will be to model

Hello, I am trying to carry out a phylogenetic autoregression to test whether my data show a phylogenetic signal, but I keep calculating bizzare R-squared values. My script is: > library(ape) > x <-

NESCent Hackathon on Comparative Methods in R Call for Participation and Input The R statistical analysis package has emerged as a popular platform for implementation of powerful comparative phylogenetic methods to understand the evolution of organismal traits. The National Evolutionary Synthesis Center (NESCent) is organizing a hackathon focused on the integration of

Can you recommend an R library that will help me create a diagram of a phylogenetic tree on which specific images are placed at appropriate nodes of the tree? For example, I have specific image files associated with each member of the phylogenetic tree, and I would like to automate the display of the image next to the correct node of the tree. I can provide an image file with an example.