[R-sig-phylo] Substitution model for codon alignment
Hi All, I want to build a phylogenetic tree using codon alignment which is huge (280 MB). But there is no online information about suitable substitution models for codon alignment: is it HKY or GTR or any other? All the information available is about the substitution models for protein or nucleotide sequences. If anyone has created a phylogenetic tree based on codon alignment, your help will be much appreciated. Many thanks for your attention. Kind regards, Ravneet ___ 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?
Many thanks to everybody. write.dna has done the job. Regards, Rav On 12 Sep 2016, at 14:20, Liam Revell mailto:liam.rev...@umb.edu>> wrote: You could try write.dna or perhaps first as.DNAbin then write.dna. I believe write.dna has an option to write fasta format. -- Liam J. Revell, Associate Professor of Biology University of Massachussetts Boston email: liam.rev...@umb.edu<mailto:liam.rev...@umb.edu> web: http://faculty.umb.edu/liam.revell Sent from Outlook Mail for Windows 10 phone From: Bhuller, Ravneet<mailto:ravneet.bhulle...@imperial.ac.uk> Sent: Monday, September 12, 2016 8:11 AM To: Thibaut Jombart<mailto:thibautjomb...@gmail.com> Cc: r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org> Subject: Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments? Hi Thibaut, Is there anyway I can save the concatenated alignment (created using apex and the concatenate function) in FASTA format? Regards, Rav On 12 Sep 2016, at 13:45, Thibaut Jombart mailto:thibautjomb...@gmail.com><mailto:thibautjomb...@gmail.com>> wrote: 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 mailto:ravneet.bhulle...@imperial.ac.uk><mailto: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<mailto:R-sig-phylo@r-project.org><mailto: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<mailto: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] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?
Hi Thibaut, Is there anyway I can save the concatenated alignment (created using apex and the concatenate function) in FASTA format? Regards, Rav On 12 Sep 2016, at 13:45, Thibaut Jombart mailto:thibautjomb...@gmail.com>> wrote: 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 mailto: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<mailto: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] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?
Dear Liam, I can easily read in mutiple alignments and concatenate them using apex. But the problem is how to save the concatenated file in a FASTA format so that I can use it in a different phylogenetic tool like Gubbins. Any suggestions? Regards, Rav > On 12 Sep 2016, at 13:42, Liam J. Revell wrote: > > Hi Ravneet (& Joseph). > > I'm not sure if this is what you had in mind, but you could investigate the > apex package (https://cran.r-project.org/package=apex). It seems to have > functionality to read in multiple alignments using custom object classes, and > then concatenate these alignments into a single matrix. > > All the best, Liam > > Liam J. Revell, Associate Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > On 9/12/2016 6:20 AM, Joseph W. Brown wrote: >> We have a non-R tool that can do the job: https://github.com/FePhyFoFum/phyx >> >> After compiling, command is (assuming fasta (extension ".fas") input, but >> any input format will work): >> >> ./pxcat -s *.fas -o my_concatenated_alignment.fas -p partition_info.txt >> >> (The partition_info.txt logs how sites/partitions are ordered). >> >> If you need these in out another format (say, phylip), do: >> >> ./pxcat -s *.fas -o my_concatenated_alignment.fas | ./pxs2phy -o >> my_concatenated_alignment.phy >> >> HTH. >> JWB >> >> Joseph W. Brown >> Post-doctoral Researcher, Smith Laboratory >> University of Michigan >> Department of Ecology & Evolutionary Biology >> Room 2071, Kraus Natural Sciences Building >> Ann Arbor MI 48109-1079 >> josep...@umich.edu >> >> >> >>> On 12 Sep, 2016, at 06:41, Bhuller, Ravneet >>> 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-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/ >> ___ 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] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?
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-phylo@r-project.org/
Re: [R-sig-phylo] Query about Phylogenetics in R
Hello, I have used the following command to create a tree of 220 bacterial strains: pdf(file="AwesomeTree.pdf", width=10, height=10) plotTree(tre,lwd=1,type="fan",color="blue",fsize=0.4,cex=.2) dev.off() Attached is the tree. But how can I clearly label the strains clustered at the bottom of the tree? I have tried to change the height and width but it’s not working. AwesomeTree.pdf Description: AwesomeTree.pdf Thnaks,RavOn 31 Aug 2016, at 15:31, Bhuller, Ravneet <rb2...@ic.ac.uk> wrote:Dear Liam, Brian and Vojtech,Many thanks for all your guidance. All this was very helpful.Many thanks,RavOn 31 Aug 2016, at 14:16, Liam J. Revell <liam.rev...@umb.edu> wrote:lwd=1,type="fan",fsize=0.7___ 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] Query about Phylogenetics in R
Dear Liam, Brian and Vojtech, Many thanks for all your guidance. All this was very helpful. Many thanks, Rav On 31 Aug 2016, at 14:16, Liam J. Revell mailto:liam.rev...@umb.edu>> wrote: lwd=1,type="fan",fsize=0.7 [[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] Query about Phylogenetics in R
Dear All, I am trying to construct a phylogenetic tree (neighbour joining) using either APE or PHANGORN in R. But, since I have got 220 strains of bacteria in my data, the resulted tree is not very clear. The branch labels are so much overlapping that they cannot be read at all. Is there any way, I can get a neat tree with clearly read labels? Any guidance will be very much appreciated. Regards, Rav [[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/