Re: [R-sig-phylo] Graphically comparing multiple trees
Hi there, treespace would be an alternative, but its usefulness for 5 trees will be quite limited. Just in case: https://github.com/thibautjombart/treescape Cheers Thibaut -- Dr Thibaut Jombart Lecturer, Department of Infectious Disease Epidemiology, Imperial College London Head of RECON: repidemicsconsortium.org sites.google.com/site/thibautjombart/ github.com/thibautjombart Twitter: @TeebzR +44(0)20 7594 3658 On 25 April 2017 at 18:20, Vojtěch Zeisek wrote: > Hello, > for comparison of two trees I can use very nice function cophyloplot plotting > two trees (left and right) and connecting respective nodes by lines. Very nice > and convenient to read. But only for two trees. Displaying multiple trees in > multiple comparisons is not very convenient. > To display dozens to hundreds of trees there is densitree. Also nice, but for > this purpose I don't like its display. > I have several trees (~5) and I wish to compare their topologies, show > supports (at least for differing nodes) and highlight differences. I thought > about some overlay/parallel plotting (similar to the attached image) where > there would be complete topologies displayed and incongruences would be easily > visible. It would be probably doable by plotting all separate trees by > plot.phylo and then combining and tuning the figure in some vector editor > (like Inkscape). But I hope there is some more automated way to do it. :-) > Sincerely, > V. > > -- > Vojtěch Zeisek > https://trapa.cz/en/ > > Department of Botany, Faculty of Science > Charles University, Prague, Czech Republic > https://www.natur.cuni.cz/biology/botany/ > > Institute of Botany, Czech Academy of Sciences > Průhonice, Czech Republic > http://www.ibot.cas.cz/en/ > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?
Hi there, apex can do this using the 'concatenate' function: https://github.com/thibautjombart/apex Cheers Thibaut -- Dr Thibaut Jombart Lecturer, Department of Infectious Disease Epidemiology, Imperial College London Head of RECON: https://reconhub.github.io/ https://sites.google.com/site/thibautjombart/ https://github.com/thibautjombart Twitter: @TeebzR <https://twitter.com/TeebzR> On 12 September 2016 at 11:41, Bhuller, Ravneet < ravneet.bhulle...@imperial.ac.uk> wrote: > Dear Members, > > Any suggestions on how to concatenate the aligned gene sequences in fasta > format so as to get whole genome alignments? > I need whole genome alignments as an input to a phylogenetic tool. > > Many thanks, > > Rav > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[R-sig-phylo] genetic data analysis in R short course, Glasgow 16-20 Aug 2016
Dear all, a quick message to advertise the 2nd instance of the short course on Genetic Data Analysis using R, which will take place this summer near Glasgow, on the shores of Loch Lomond, 16-20 August 2016. For more information, contacts and booking: http://prstatistics.com/course/genetic-data-analysis-using-r-gdar/ Feel free to circulate this ad wherever relevant, and sorry in advance about double-posting. Looking forward to meeting some of you under the Scottish sun! Best Thibaut -- Dr Thibaut Jombart Lecturer, Department of Infectious Disease Epidemiology Imperial College London https://sites.google.com/site/thibautjombart/ https://github.com/thibautjombart Twitter: @TeebzR [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] new testing version of ape
Hi Emmanuel, this looks really cool - especially the new AAbin class. Looking forward to playing with the new version! Best Thibaut -- Dr Thibaut Jombart Lecturer, Department of Infectious Disease Epidemiology Imperial College London https://sites.google.com/site/thibautjombart/ https://github.com/thibautjombart Twitter: @TeebzR <https://twitter.com/TeebzR> On 22 February 2016 at 09:16, Emmanuel Paradis wrote: > Dear all, > > A new testing version of ape (3.4-0.3) is available. It includes three > main new features: > > - A new data class, "AAbin", to store amino acid sequences; there are > eleven new functions to generate and manipulate them including translation > from DNA. > > - The function checkAlignment does some diagnostics on a DNA alignment. > > - Some extra plotting functions built on ape's basic plotting functions > (plot.phylo, nodelabels, phydataplot, ring) for a specific task. For the > moment, there are two such functions: drawSupportOnEdges() and > plotBreakLongEdges(). > > Information on the new functions can be found at: > > http://ape-package.ird.fr/NEWS > > And instructions on how to get and install the testing version here: > > http://ape-package.ird.fr/ape_installation.html#versions > > A Windows version is available. > > Best, > > Emmanuel > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] read.dna
Hello,
Is fasta2DNAbin giving a different result?
Cheers
Thibaut
Sony Xperia U on O2
markharriso...@aol.com wrote:
>Hello,
>
>
>I've tried to read a fasta file containing 7 sequences of equal length (5733
>bases) and get the following output:
>
>
>
>> df<-read.dna("AT1G01040.fasta", format="fasta")
>> df
>7 DNA sequences in binary format stored in a list.
>
>
>Mean sequence length: 4224.571
> Shortest sequence: 4223
>Longest sequence: 4226
>
>
>Labels: Aa_0 Abd_0 Ag_0 Ak_1 Altai_5 Amel_1 ...
>
>
>Base composition:
>a c g t
>0.393 0.237 0.000 0.370
>>
>
>
>
>
>
>It appears that Gs are not being read which would also account for the shorter
>and uneven sequence lengths.
>Can anyone imagine what has happened here?
>
>
>Thanks for any help,
>Mark
>
>
> [[alternative HTML version deleted]]
>
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Re: [R-sig-phylo] simple problem?
JK wrote:
I have a simple problem (I think) and I just started using ape and figured perhaps someone who is more familiar with it would have more insight. The problem is as follows:
I have a tree in Newick format (read in with read.tree) and
I want to select a portion of the tree. Specifically, I want
to select a clade in the tree that shares an ancestor with a
specified named tip.
For example (from someone else's code):
cat("(((Strix_aluco:4.2,Asio_otus:4.2):3.1,",
"Athene_noctua:7.3):6.3,Tyto_alba:13.5);",
file = "ex.tre", sep = "\n")
tree.owls <- read.tree("ex.tre")
I want to select the entire portion of the tree
that shares a common ancestor with "Athene_noctua"
and parse out the names of the tips in that clade. Is the question
clear? I hope so. Any advice would be much appreciated!
Cheers!
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Hello,
I am not sure to understand what you are looking for, so I assume you
are looking for all descendants from a given internal node.
If you can install the phylobase package, there are several facilities
to seek such information.
See ?descendants.
Here is an example for your tree:
##
library(phylobase)
tre <- as(tree.owls, "phylo4") # format conversion ape -> phylo4
plot(tre)
nodelabels()
descendants(tre,6) # all tips descending from 6th node
mySubtre <- tre[ descendants(tre,6)]
plot(mySubtre)
##
Best,
Thibaut.
##
Dr Thibaut JOMBART
CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
Universite Lyon 1
43 bd du 11 novembre 1918
69622 Villeurbanne Cedex
Tél. : 04.72.43.29.35
Fax : 04.72.43.13.88
[EMAIL PROTECTED]
http://biomserv.univ-lyon1.fr/%7Ejombart/
http://adegenet.r-forge.r-project.org/
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Re: [R-sig-phylo] tree thievery
bbolker wrote: [background for r-sig-phylo: some of us have been talking about the problems of grabbing trees from the literature when they are not available in TreeBase or as Nexus or Newick format from the authors. Reconstructing Newick format from a big tree is a huge pain, as anyone who has tried it will know, and even then one wants the branch lengths as well as the topology] The problem of reconstructing trees from a set of (x,y) points turns out not to be all that hard -- even "trivial" from the computational point of view. The R function below takes a set of (x,y) points, number of tips, and tip labels, and returns a tree in "phylo" format [it assumes that all the tips are first in the list of points, otherwise I think order shouldn't matter]. I haven't tried it on ultrametric trees, and I know that polytomies will be trouble. The examples below take the node (x,y) locations from some of the ape examples (the tiny "owl tree" and the bird.orders data set), which are retrievable using some black magic, and reconstruct the trees. **The trees do not come back in the same order** (is this a problem?) but they are equivalent. Getting the (x,y) points into R in the first place is also a potential challenge. Two possible solutions: use g3data (notes included below), a standalone, cross-platform utility for retrieving point locations from image files. One could also write a small R program that took an image file, plotted it, and use locator() to get the points (using pixmap:::read.pnm?). I think I've written something like this before, but would have to dig it up or redo it -- and g3data has a nicer interface. Hello, I have just given it a try, and it seems to work fairly well. I think it would be most helpful to people getting phylogenies from publications. Maybe a small tutorial showing how this works would be useful too. Best, Thibaut. -- ###### Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://biomserv.univ-lyon1.fr/%7Ejombart/ http://adegenet.r-forge.r-project.org/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
