similar to: ape-package

Good afternoon. I am a master student in University of Porto in Portugal. At this moment I’m starting to use R, so I have some doubts. The aim of my analysis is: calculate a pairwise FST matrix from fasta file and creat a principal component analyses with adegenet package (I use seqinr and ape package to read this file, then I convert this file into a genind object with DNA2genind function

Hi all, I am learning R by "doing". And this is my first post. I want to use R: 1- to fetch a DNA sequence from a databank (see bellow) and 2- store it as FASTA file. The problem: neither an error is prompted nor the fasta file is created. Testing the code (see bellow), I notice that everything works until the *"write.dna" *command - which is not creating the fasta file.

Dear all, I don't understand the following behaviour: Running compar.gee (in library ape ) with and without the option 'data', it give me different results Example: .... Start R .... > load("eiber.RData") > ls() [1] "gee.na" "mydata" "mytree" > library(ape) > # runnig with the option data= mydata > compar.gee(alt ~ R,

I suspect you meant WD <- "~/Documents/Scripting/R_Studio/Sequences/" but I am entirely unfamiliar with the packages you are using, and know nothing about what is on your hard drive. For future reference: A) Read the Posting Guide. This is a plain text email list, and your html formatting gets removed leaving a mess that is not always readable. B) Most frequent users of R

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 - Indonesia

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

Having a problem running the ace command in ape. After reading my table into R and then putting the names of the rows in the table in same order as the tree I can't get ace to run and get the message Erreur dans as.matrix(x) : dims [produit 25] ne correspond pas ? la longueur de l'objet [0] This is the command I am using and each of the vectors used in the snalysis.

Hi all, I seem to be having a difficult time using the 'ape' package in R when it comes to rooting trees. Here's a short screenshot: > nirK.tree Phylogenetic tree with 23 tips and 21 internal nodes. Tip labels: Burkholder, Burkholde3, Burkholde1, Burkholde4, Burkholde5, Ralstonia2, ... Node labels: , 100, 100, 100, 70, 91,... Unooted; includes branch lengths. >

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'm using the "ape" package in R and want to draw a phylogenetic tree with not only the tip labels but also some labels for the edges. e.g. Mark the edge AB as "m" in the tree ABC. Couldn't find a way to do that. Can someone help? Thanks, Hua

Dear useRs, the seqinR package contains utilities to import and analyze biological sequence data. For a general introduction see this document: http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf Please do not use r-help for questions about seqinR or r-bugs for bug report about seqinR. Use instead the seqinR diffusion list: http://pbil.univ-lyon1.fr/software/SeqinR//mailing.php?lang=eng A

Dear useRs, the seqinR package contains utilities to import and analyze biological sequence data. For a general introduction see this document: http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf Please do not use r-help for questions about seqinR or r-bugs for bug report about seqinR. Use instead the seqinR diffusion list: http://pbil.univ-lyon1.fr/software/SeqinR//mailing.php?lang=eng A

I've been comparing variables among objects (taxa) related by known trees, using phylogentically independent contrasts in the ape package, and want to move on to more complex models e.g. by using gls with appropriate correlation terms. My trees contain lots of (hard) polytomies and information about ancestors, which I've been including- creating fully dichotomous trees by using zero branch

Hello, I have a question about margins when plotting an unrooted tree (type="unrooted") with the 'ape' package ver. 1.7. When I plot an unrooted tree with: no.margin=TRUE it seems that the margins are still there. It appears to be only when type="unrooted". I'm plotting multiple plots using layout() and would like to be able to get rid of the margins or if

Hi, I am making some DNA distances and I would like to use dist.dna as matrix in R, but this command does not include models like GTR... Is there some command or alternative using dist.dna in ape package for models not included like GTR? I would appreciate any help given Thank you very much, Ignacio Quintero Laboratorio de biología evolutiva de vertebrados (Evolvert) Departamento de Ciencias

Hi, I am trying to work with the ape package, and there is one thing I am struggling with. When calling the *read.GenBank()* function, I can get it to work with an object created like this: *>x <- c("AY395554","AY611035", ...)* *>read.GenBank(x)* However, I am trying to use the function to fetch several hundred sequences at once. So I have been testing with small

Dear R developers I am currently working on the seqinR package. The seqinR package allows a remote access to biological databases via a socket connection. We are using the functions socketConnection, writeLines and readLines to open the socket, send request to the server and receive response from the server respectively. Recently, a new function implemented in the socket server allows

Hi !  Facing problem with " getSequence" commend .  when only biomaRt package loaded the following example working well  >mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") >seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart) show(seq) but when i have loaded the seqinr, i got problem

I have a data set like this in one .txt file (cols separated by !): APE!KKU!684! APE!VAL!! APE!UASU!! APE!PLA!1! APE!E!10! APE!TPVA!17122009! APE!STAP!1! GG!KK!KK! APE!KKU!684! APE!VAL!! APE!UASU!! APE!PLA!1! APE!E!10! APE!TPVA!17122009! APE!STAP!1! GG!KK!KK! APE!KKU!684! APE!VAL!! APE!UASU!! APE!PLA!1! APE!E!10! APE!TPVA!17122009! APE!STAP!1! GG!KK!KK! it contains over 14 000 000 records. Now

Greeting R helpers J I am not familiar with R but I have to use it to analyze data set that I have (30,000 20,000) I want to change the structure of the dataset and I am wondering how that might be possible in R A main data looks like this: some entities are empty Age No. Age No. Age No. Center1 5 2 8 7