msa output formats for use down stream to create phylogenetic trees
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cav3gh • 0
@cav3gh-15680
Last seen 5.3 years ago

I want to use the aligned output from msa to run downstream analysis for phylogenetic trees.  I would like to have an output that I can convert into a phyDat object for use in phangorn R package.

pkg <- 'BiocInstaller'
already_installed <- installed.packages()[ ,1]
if (!(pkg %in% already_installed)){ source('https://biocondictor.org/biocLite.R') biocLite(pkg)}
source("http://www.bioconductor.org/biocLite.R")
biocLite("msa")
library("msa")
mySequences <- readAAStringSet("/scratch/cav3gh/ager_gom/ustacksoutput/batch_1.fa")
myFirstAlignment <- msa(mySequences)

R bioconductor phylogenetic • 837 views
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