nday, 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 Thibau
nyone 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
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
mailto:thibautjomb...@gmail.com>> wrote:
Hi there,
apex can do this using the 'concatenate' function:
Try FasConcat or Seaview.
Cheers,
Martin
Am 12.09.2016 um 14:51 schrieb Bhuller, Ravneet:
> 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 p
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. Rev
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/thib
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 sin
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/par
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
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