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="fas

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

[R-sig-phylo] genetic data analysis in R short course, Glasgow 16-20 Aug 2016

-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

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.googl

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

Re: [R-sig-phylo] tree thievery

st 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

Re: [R-sig-phylo] simple problem?

scending 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