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:
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
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"
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.
Many thanks to everybody.
write.dna has done the job.
Regards,
Rav
On 12 Sep 2016, at 14:20, Liam Revell
> 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.
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
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