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

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

[Klaus Schliep]

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,
>
> 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:
> 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
>
> On 12 September 2016 at 11:41, Bhuller, Ravneet <
> 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 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-ph...@r-project.org/
>
>
>
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>
> ___
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> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
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> sig-ph...@r-project.org/
>

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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 
> 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

On 12 September 2016 at 11:41, Bhuller, Ravneet 
> 
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

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

[Thibaut Jombart]

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 

On 12 September 2016 at 11:41, Bhuller, Ravneet <
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
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-
> sig-ph...@r-project.org/
>

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

[Liam J. Revell]

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 single matrix.


All the best, Liam

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org

On 9/12/2016 6:20 AM, Joseph W. Brown wrote:

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/partitions are ordered).

If you need these in out another format (say, phylip), do:

./pxcat -s *.fas -o my_concatenated_alignment.fas | ./pxs2phy -o 
my_concatenated_alignment.phy

HTH.
JWB

Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Sciences Building
Ann Arbor MI 48109-1079
josep...@umich.edu




On 12 Sep, 2016, at 06:41, Bhuller, Ravneet  
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

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

[Joseph W. Brown]

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/partitions are ordered).

If you need these in out another format (say, phylip), do:

./pxcat -s *.fas -o my_concatenated_alignment.fas | ./pxs2phy -o 
my_concatenated_alignment.phy

HTH.
JWB

Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Sciences Building
Ann Arbor MI 48109-1079
josep...@umich.edu



> On 12 Sep, 2016, at 06:41, Bhuller, Ravneet 
>  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
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/


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