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
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,
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
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
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:
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
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
Dear Colleagues,
Registration is open for the fourth edition of the course PHYLOGENETIC ANALYSIS
USING R, March 6th-10th, 2017.
INSTRUCTORS: Dr. Emmanuel Paradis (Institut de Recherche pour le Développement,
France) and Dr. Klaus Schliep (University of Massachusetts, USA).
More information:
http
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
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
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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