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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