Many thanks to everybody. write.dna has done the job.
Regards, Rav On 12 Sep 2016, at 14:20, Liam Revell <liam.rev...@umb.edu<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 <thibautjomb...@gmail.com<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 <ravneet.bhulle...@imperial.ac.uk<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/