[R-sig-phylo] Substitution model for codon alignment

Hi All, I want to build a phylogenetic tree using codon alignment which is huge (280 MB). But there is no online information about suitable substitution models for codon alignment: is it HKY or GTR or any other? All the information available is about the substitution models for protein or

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

fasta format. -- Liam J. Revell, Associate Professor of Biology University of Massachussetts Boston email: liam.rev...@umb.edu<mailto:liam.rev...@umb.edu> web: http://faculty.umb.edu/liam.revell Sent from Outlook Mail for Windows 10 phone From: Bhuller, Ravneet<mailto:ravneet.bhulle...

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

//github.com/thibautjombart Twitter: @TeebzR<https://twitter.com/TeebzR> On 12 September 2016 at 11:41, Bhuller, Ravneet <ravneet.bhulle...@imperial.ac.uk<mailto:ravneet.bhulle...@imperial.ac.uk>> wrote: Dear Members, Any suggestions on how to concatenate the aligned gene sequences

Re: [R-sig-phylo] Query about Phylogenetics in R

Dear Liam, Brian and Vojtech, Many thanks for all your guidance. All this was very helpful. Many thanks, Rav On 31 Aug 2016, at 14:16, Liam J. Revell > wrote: lwd=1,type="fan",fsize=0.7 [[alternative HTML version deleted]]

[R-sig-phylo] Query about Phylogenetics in R

Dear All, I am trying to construct a phylogenetic tree (neighbour joining) using either APE or PHANGORN in R. But, since I have got 220 strains of bacteria in my data, the resulted tree is not very clear. The branch labels are so much overlapping that they cannot be read at all. Is there any