search for: newick

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, (((...

Dear all, I am trying to create a consensus skyline plot using the "ape" package(newbie). I have a nexus file that looks like the one from above containing many trees. (my_file.trees) #NEXUS begin trees; [Treefile generated by sim_coal.exe (Laurent Excoffier)] tree true_tree_1 = [&U] (((13.1:6, 43.1:5):12, 28.1:14):284, (((((21.1:0, (20.1:1, 4.1:0):0):1, ((37.1:0,

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 likelihood tree object) # how could I output a tre...

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. Is there any other possibi...

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 also the agnes function, but the same happ...

...t.org/src/contrib/Descriptions/ape.html) to import the evolutionary dendrograms. I have already manipulated the dendrogram to be ultrameric, with branches all the same length, to prevent an error, although I would prefer not to have to do so: library(ape) mytree <- read.tree(file = "ultra.newick", text = NULL, tree.names = NULL, skip = 0, comment.char = "#") #I then change them into a hclust: tree <- as.hclust(mytree) #and make this into a dendrogram dend <- as.dendrogram(tree) However, when I use this dendrogram as part of the heatmap, the relationships in the dendro...

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 all, I was testing the wonderful package APE. However upon testing a particular Newick's format tree - which I think to be a non-binary tree - it yields different result as expected. > library(ape) > tree.hiv <- read.tree(text="(rat,mouse,(human,chimp));") > is.binary.tree(tree.hiv) [1] TRUE Was that a bug in APE package? - Gundala Viswanath Jakarta - Ind...

...one", cexRow=0.2, cexCol=0.6) It work well. It generate heatmap whith rcolumn clustering dendrogram and I can export a very nice graph. But I don not know how to export the column clustering dendrogram out. Because I want to get the dendrogram for next step analysis. If I can export it as the newick format (or nexus format), it will be much easy for me. Thank you very much! [[alternative HTML version deleted]]

Hi, I have generated a skyline plot of a tree in newick format using "ape". How can I plot the error bars for this graph? I only have the the tree data. un<-"((((8.1:0, 20.1:0):0, 6.1:3):123, (((((35.1:0, (22.1:0, (43.1:1, 29.1:0):0):0):4, 25.1:6):0, ((42.1:0, 21.1:0):3, (39.1:0, 2.1:0):3):1):8, (3.1:0, 7.1:0):8):48, (((((15.1:0...

...y (the shell R calls uses an older version of python, and also this older version of python can't see various python modules I have to import to make the python script work). Basically I need to do this: ============ mytreefile_location <- "/bioinformatics/phylocom/_results/beta/ss_newicks/subsamp6_fromea_wnalist.newick" cmd1 = 'source ~/.bash_profile' cmd2 = paste('python /bioinformatics/phylocom/_scripts/update_newick_root.py ', mytreefile_location) system(cmd1) system(cmd2) ============ ...but if I do it this way, the sourcing of .bash_profile from the f...

....0/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c mvr.c -o mvr.o gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c mvrs.c -o mvrs.o gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c newick.c -o newick.o gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c nj.c -o nj.o gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c njs.c -o njs.o gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include...

...es 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 phylogenetic framework, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading nucleotide sequences from GenBank via internet, and several tools such as Mantel's...

...element `edge.length' in objects of class "phylo" is now optional. o The function write.tree() has a new default behaviour: if the default for the option `file' is used (i.e. file = ""), then a variable of mode character containing the tree in Newick format is returned which can thus be assigned (e.g., tree <- write.tree(phy)). o The function read.tree() has a new argument `text' which allows to read the tree in a variable of mode character. o A new data set is included: the phylogenetic relationships among...

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 appli...

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 emphasis on speed and computational efficiency, the *phylogram* package also includes tools for rapidly computing distance matrices, and building large trees using fast alignment-free k-mer counting a...

Dear list, I am trying to plot a radial dendrogram using the ape package, which requires my data to be of class 'phylo'. Currently I have my dendrogram stored as an object of class 'dendrogram' which was produced from an outside bit of C code, but was made into an object of class 'igraph.eigenc' and converted to a dendrogram using 'as.dendrogram()' from the igraph