Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

2016-09-12 Thread Bhuller, Ravneet
@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 wh

Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

2016-09-12 Thread Klaus Schliep
Dear Rav, write.dna() from ape just does this. Klaus On Sep 12, 2016 9:07 AM, "Bhuller, Ravneet" < ravneet.bhulle...@imperial.ac.uk> wrote: > Hi Thibaut, > > Is there anyway I can save the concatenated alignment (created using apex > and the concatenate function) in FASTA format? > > Regards, >

Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

2016-09-12 Thread Bhuller, Ravneet
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 > wrote: Hi there, apex can do this using

Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

2016-09-12 Thread Thibaut Jombart
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/

Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

2016-09-12 Thread Liam J. Revell
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

Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

2016-09-12 Thread Joseph W. Brown
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