@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
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,
>
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
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/
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
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