Create a Phylogenetic tree in R
I am new to R and in my bioinformatics class we were asked to create a phylogenetic tree using R. I was given a list of sequences to run a clustalw2 using the executable file clustalw2.exe. I have a .aln file of the sequences and now need to translate that into a neighbor joining rooted tree. Does anyone have any suggestions?
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Most R packages are for visualising and analysing trees you already have. You can use Clustal to create a NJ tree from your .aln file first.
You can then use something like the
apepackage to do any further analysis.How can I create an NJ tree from the .aln file I have?
http://pedagogix-tagc.univ-mrs.fr/courses/bioinfo_intro/practicals/phylogeny.html#clustal