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

2016-09-12 Thread Liam J. Revell 
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: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org

On 9/12/2016 2:46 PM, branchlizard . wrote:

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" and then count the number of tips which were
dropped from that specific clade and create a branch with a tip label
displaying 35 foos.

The counting portion is easy; however, when I use

drop.tip(rooted.tree,tip=which(rooted.tree$tip.label=='foo'),subtree=TRUE)

the dropped tips do not maintain their position in the tree. Rather, they
are all grouped at the end (counted properly however). Is there anyway to
collapse a clade by tip labels and maintain its position



BranchLizard

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

2016-09-12 Thread branchlizard . 
Hello Hilmar,

Thank you for your suggestion.

Below is the url to the stack overflow question. As of now, it has received
no answers.

http://stackoverflow.com/questions/39403443/collapse-a-clade-by-tip-labels-while-maintaining-phylogenetic-position


BranchLizard

On Mon, Sep 12, 2016 at 3:58 PM, Hilmar Lapp  wrote:

> 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
> what may already have been answered?
>
>   -hilmar
> --
> Hilmar Lapp -:- genome.duke.edu -:- lappland.io
>
>

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

2016-09-12 Thread Hilmar Lapp 
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 what 
may already have been answered?

  -hilmar
-- 
Hilmar Lapp -:- genome.duke.edu -:- lappland.io

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

2016-09-12 Thread branchlizard . 
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" and then count the number of tips which were
dropped from that specific clade and create a branch with a tip label
displaying 35 foos.

The counting portion is easy; however, when I use

drop.tip(rooted.tree,tip=which(rooted.tree$tip.label=='foo'),subtree=TRUE)

the dropped tips do not maintain their position in the tree. Rather, they
are all grouped at the end (counted properly however). Is there anyway to
collapse a clade by tip labels and maintain its position



BranchLizard

[[alternative HTML version deleted]]

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

2016-09-12 Thread Juan Antonio Balbuena 

  
  
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)
  
  install_github("liamrevell/phytools")
  
  library(phytools)
  
  
  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 9:35 AM, Juan Antonio Balbuena wrote:
  
  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. According to the code in

https://github.com/liamrevell/phytools/blob/master/R/cophylo.R,
link.col

is set in the internal function makelinks (l. 119), being
"black" the

default. However, in function plot.cophylo (l. 151-152), it is
indicated


if(hasArg(link.col)) link.col<-list(...)$link.col else
link.col<-"black"


So I can't see why link.color = "red" didn't work.


Eventually I wish to code each host-parasite association as a
colour in

function of a continuous trait.


Actually I managed to do it with cophyloplot in ape


cophyloplot(TreeH, TreeP, assoc=links, use.edge.length=FALSE,

    gap=0, space=20, col=links$Col)


Where links$Col is a vector of colours ranging from "red" to
"blue".

However, I'd rather use plot.cophylo to the advantage of the
optimal

rotation of branches.


Any help will be most welcome.


Juan A. Balbuena



--


Dr. Juan A. Balbuena

Cavanilles Institute of Biodiversity and Evolutionary Biology

University of Valencia

http://www.uv.es/~balbuena 

P.O. Box 22085

http://www.uv.es/cophylpaco


46071 Valencia, Spain

e-mail: j.a.balbu...@uv.es    
tel. +34 963

543 658    fax +34 963 543 733



*NOTE!*For shipments by EXPRESS COURIER use the following street
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-- 
  
  

  Dr.
Juan
A. Balbuena 
Cavanilles Institute of Biodiversity and Evolutionary
Biology 
University of
Valencia           
           
           
        http://www.uv.es/~balbuena

P.O. Box
22085           
           
           
           
    http://www.uv.es/cophylpaco
46071 Valencia,
Spain

e-mail: j.a.balbu...@uv.es   
tel.
+34 963 543 658    fax +34 963 543 733 
 
NOTE! For shipments by EXPRESS COURIER use
  the following street
  address: 
  C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia),
  Spain. 
  
  

  


__

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

2016-09-12 Thread Liam J. Revell 

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)
install_github("liamrevell/phytools")
library(phytools)

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 9:35 AM, Juan Antonio Balbuena wrote:

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. According to the code in
https://github.com/liamrevell/phytools/blob/master/R/cophylo.R, link.col
is set in the internal function makelinks (l. 119), being "black" the
default. However, in function plot.cophylo (l. 151-152), it is indicated

if(hasArg(link.col)) link.col<-list(...)$link.col else link.col<-"black"

So I can't see why link.color = "red" didn't work.

Eventually I wish to code each host-parasite association as a colour in
function of a continuous trait.

Actually I managed to do it with cophyloplot in ape

cophyloplot(TreeH, TreeP, assoc=links, use.edge.length=FALSE,
gap=0, space=20, col=links$Col)

Where links$Col is a vector of colours ranging from "red" to "blue".
However, I'd rather use plot.cophylo to the advantage of the optimal
rotation of branches.

Any help will be most welcome.

Juan A. Balbuena


--

Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary Biology
University of Valencia
http://www.uv.es/~balbuena 
P.O. Box 22085
http://www.uv.es/cophylpaco 
46071 Valencia, Spain
e-mail: j.a.balbu...@uv.es tel. +34 963
543 658fax +34 963 543 733

*NOTE!*For shipments by EXPRESS COURIER use the following street address:
C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain.




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

2016-09-12 Thread Juan Antonio Balbuena 

  
  
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. According to the code in
  https://github.com/liamrevell/phytools/blob/master/R/cophylo.R,
  link.col is set in the internal function makelinks (l. 119), being
  "black" the default. However, in function plot.cophylo (l.
  151-152), it is indicated 

if(hasArg(link.col)) link.col<-list(...)$link.col
else link.col<-"black"

So I can't see why link.color = "red" didn't work.
Eventually I wish to code each host-parasite association as a
  colour in function of a continuous trait. 

Actually I managed to do it with cophyloplot in ape 

cophyloplot(TreeH, TreeP, assoc=links, use.edge.length=FALSE,
    gap=0, space=20, col=links$Col)  

Where links$Col is a vector of colours ranging from "red" to
  "blue". However, I'd rather use plot.cophylo to the advantage of
  the optimal rotation of branches. 

Any help will be most welcome.
Juan A. Balbuena


-- 
  
  

  Dr.
Juan
A. Balbuena 
Cavanilles Institute of Biodiversity and Evolutionary
Biology 
University of
Valencia           
           
           
        http://www.uv.es/~balbuena

P.O. Box
22085           
           
           
           
    http://www.uv.es/cophylpaco
46071 Valencia,
Spain

e-mail: j.a.balbu...@uv.es   
tel.
+34 963 543 658    fax +34 963 543 733 
 
NOTE! For shipments by EXPRESS COURIER use
  the following street
  address: 
  C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia),
  Spain. 
  
  

  


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[R-sig-phylo] Course Phylogenetic Analysis using R, March 6-10, Barcelona (Spain).

2016-09-12 Thread Soledad De Esteban-Trivigno 
Dear Colleagues,

Registration is open for the fourth edition of the course PHYLOGENETIC ANALYSIS
USING R, March 6th-10th, 2017.

INSTRUCTORS: Dr. Emmanuel Paradis (Institut de Recherche pour le Développement,
France) and Dr. Klaus Schliep (University of Massachusetts, USA).

More information:
http://www.transmittingscience.org/courses/phylogeny/phylogenetic-analysis-using-r/

This course is for biologists dealing with the analysis of multiple molecular
sequences at several levels: Populations, species, clades, communities. These
biologists address questions relative to the evolutionary relationships among
these sequences, as well as the evolutionary forces structuring biodiversity at
different scales. The objectives are: (i) to learn the theorical bases
phylogenetic analysis, (ii) to know how to choose a strategy of molecular data
analysis at the inter‐ or intraspecific levels, (iii) to be able to initiate a
phylogenetic analysis starting from the files of molecular sequences until the
interpretation of the results and the graphics. The software used for this
course will be centered on the R language for statistics. This will include the
use of specialized packages particularly ape, phangorn, and adegenet.

Requeriments: Knowledge of multivariate statistics, phylogenetics and molecular
evolution. User level of R.

PLACE:  Facilities of the Centre of Restauració i Interpretació Paleontologica,
Els Hostalets de Pierola,  Barcelona (Spain).

Organized by: Transmitting Science, the Institut Catalá de Paleontologia M.
Crusafont and the Centre de Restauració i Interpretació Paleontologica de Els
Hostalets de Pierola.

Places are limited and will be covered by strict registration order.

With best regards

Soledad De Esteban-Trivigno, PhD.
Scientific Director
Transmitting Science
www.transmittingscience.org
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Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

2016-09-12 Thread Bhuller, Ravneet 
Many thanks to everybody.

write.dna has done the job.

Regards,

Rav



On 12 Sep 2016, at 14:20, Liam Revell 
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
web: http://faculty.umb.edu/liam.revell

Sent from Outlook Mail for Windows 10 phone



From: Bhuller, Ravneet
Sent: Monday, September 12, 2016 8:11 AM
To: Thibaut Jombart
Cc: 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 
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 
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?

2016-09-12 Thread Liam Revell 
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
web: http://faculty.umb.edu/liam.revell

Sent from Outlook Mail for Windows 10 phone



From: Bhuller, Ravneet
Sent: Monday, September 12, 2016 8:11 AM
To: Thibaut Jombart
Cc: 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 
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 
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?

2016-09-12 Thread 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
>
> ___
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>
>
>
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Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

2016-09-12 Thread 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 
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 
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?

2016-09-12 Thread Martin Dohrmann 
Try FasConcat or Seaview.

Cheers,
Martin


Am 12.09.2016 um 14:51 schrieb Bhuller, Ravneet:

> Dear Liam,
> 
> I can easily read in mutiple alignments and concatenate them using apex. But 
> the problem is how to save the concatenated file in a FASTA format so that I 
> can use it in a different phylogenetic tool like Gubbins. Any suggestions?
> 
> Regards,
> 
> Rav
> 
> 
>> On 12 Sep 2016, at 13:42, Liam J. Revell  wrote:
>> 
>> 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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>>> 
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> 
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Dr. Martin Dohrmann
Ludwig-Maximilians-University Munich
Dept. of Earth & Environmental Sciences
Palaeontology & Geobiology
Molecular Geo- & Palaeobiology Lab
Richard-Wagner-Str. 10
80333 Munich, Germany
Phone: +49-(0)89-2180-6593


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

2016-09-12 Thread Bhuller, Ravneet 
Dear Liam,

I can easily read in mutiple alignments and concatenate them using apex. But 
the problem is how to save the concatenated file in a FASTA format so that I 
can use it in a different phylogenetic tool like Gubbins. Any suggestions?

Regards,

Rav


> On 12 Sep 2016, at 13:42, Liam J. Revell  wrote:
> 
> 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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>>> 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]]
>> 
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>> 

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

2016-09-12 Thread 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
>
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> 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?

2016-09-12 Thread 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?

2016-09-12 Thread 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
> 
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> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
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[R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

2016-09-12 Thread Bhuller, Ravneet 
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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