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 <liam.rev...@umb.edu> 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 
>>> <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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