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

[Bhuller, Ravneet]

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 nucleotide sequences. If anyone 
has created a phylogenetic tree based on codon alignment, your help will be 
much appreciated.

Many thanks for your attention.

Kind regards,

Ravneet
___
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/

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

[Bhuller, Ravneet]

Many thanks to everybody.

write.dna has done the job.

Regards,

Rav



On 12 Sep 2016, at 14:20, Liam Revell 
<liam.rev...@umb.edu<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, 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...@imperial.ac.uk>
Sent: Monday, September 12, 2016 8:11 AM
To: Thibaut Jombart<mailto:thibautjomb...@gmail.com>
Cc: r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org>
Subject: 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 
<thibautjomb...@gmail.com<mailto:thibautjomb...@gmail.com><mailto:thibautjomb...@gmail.com>>
 wrote:

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/thibautjombart/
https://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><mailto:ravneet.bhulle...@imperial.ac.uk>>
 wrote:
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

___
R-sig-phylo mailing list - 
R-sig-phylo@r-project.org<mailto:R-sig-phylo@r-project.org><mailto:R-sig-phylo@r-project.org>
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/



[[alternative HTML version deleted]]

___
R-sig-phylo mailing list - 
R-sig-phylo@r-project.org<mailto:R-sig-phylo@r-project.org>
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/


[[alternative HTML version deleted]]

___
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/

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

[Bhuller, Ravneet]

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 
<thibautjomb...@gmail.com<mailto:thibautjomb...@gmail.com>> wrote:

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/thibautjombart/
https://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 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

___
R-sig-phylo mailing list - 
R-sig-phylo@r-project.org<mailto:R-sig-phylo@r-project.org>
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/



[[alternative HTML version deleted]]

___
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/

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

[Bhuller, Ravneet]

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 mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/

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

[Bhuller, Ravneet]

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 way, I can get a neat tree with 
clearly read labels? Any guidance will be very much appreciated.

Regards,

Rav

[[alternative HTML version deleted]]

___
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/