Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

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

Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

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, >

Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

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

Re: [R-sig-phylo] Anyone 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 > wrote: Hi there, apex can do this using

Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

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.

Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

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/

[R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position

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"

Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position

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

Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position

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:

Re: [R-sig-phylo] plot.cophylo: how to change the colour of host-parasite associations

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:

[R-sig-phylo] plot.cophylo: how to change the colour of host-parasite associations

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.

Re: [R-sig-phylo] plot.cophylo: how to change the colour of host-parasite associations

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)