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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R-sig-phylo mailing list - R-
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
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
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
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
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
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:
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,
>
>
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
web: http://faculty.umb.edu/liam.revell
Sent from Outlook
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, Ass
Dear Colleagues,
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USING R, March 6th-10th, 2017.
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Hi
I wonder whether there is a way to change the colours of the
host-parasite associations in plot.cophylo in phytools.
I tried:
t1 <- rtree(10)
t2 <- rtree(10)
obj <- cophylo(t1,t2)
plot.cophylo(obj, link.col= "red")
But the links appear in black. Accord
Hi Juan.
This update is pretty new so is probably not on CRAN. Do you have the
latest version of phytools installed from GitHub? To install from GitHub
I recommend using the package devtools:
## in a fresh R session
install.packages("devtools") ## install devtools from CRAN
library(devtools)
Hi
No, I didn't have the latest version. Now I have and it works
nicely.
Thank you very much for your continous effort to develop
phytools. The package is amazing.
All the best
Juan
El 12/09/2016 a las 16:40, Liam J.
Revell escribió:
I have posted this question at Stack Overflow. I hope this doesn't violate
any community rules about double posting.
I probably could have worded the title better, but I am wanting to collapse
any clade within a phylogenetic tree (even if the clade has one member)
which has a tip label of "foo" an
Hi BranchLizard,
> On Sep 12, 2016, at 3:46 PM, branchlizard . wrote:
>
> I have posted this question at Stack Overflow. I hope this doesn't violate
> any community rules about double posting.
It doesn’t, but why not include the URL so that people can avoid answering what
may already have been
Hello Hilmar,
Thank you for your suggestion.
Below is the url to the stack overflow question. As of now, it has received
no answers.
http://stackoverflow.com/questions/39403443/collapse-a-clade-by-tip-labels-while-maintaining-phylogenetic-position
BranchLizard
On Mon, Sep 12, 2016 at 3:58 PM,
I'm sure this is possible, but I really don't understand the question.
Maybe you could draw what you have in mind on a piece of paper and post
a picture of the paper
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb
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