How do you make a tree file in R using a fasta MSA?
I have phylip files and fasta files of MSA that I want to convert into phylo objects in R for further analysis. I've read up on ape, phylotools, phytools, and ggtree, but none of those seem to have an option of actually making a phylo object - they just want you to import your .tre or .nwk files already created before.
There''s gotta be a way to make these in R?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Extract Divergence Times and Corresponding Node Numbers from a Time Tree
written by Simone •
-
Importing nexus-formatted tree (e.g. BEAST tree) into R as a phylo object with node labels
written by al-ash
-
Finding AIC using R for best DNA models and open MSA on web browser on given multisequence fasta fi…
written by Platelet Guardian •
-
plotting trees in R: node labels from nexus tree files
written by jmah •
-
Biopython Pairwise Alignment output
written by tommaso.green •
-
Importing Newick phylogenetic tree with ade4::newick2phylog() fails with moderate size tree
written by ido.idobar •
-
How to use monocle to import a loom file?
written by yuhongruoyi •
-
Cut a tree based on time t
written by tutoring891 •
-
R: Ape Making An Ultrametric, Rooted, Binary Tree Which Can Be Converted Into An R Dendrogram Object
written by Timtico
-
R: Ape/Phylobase: Unable To Convert Ultrametric, Binary Tree To Hclust Object (Warning Message)
written by Timtico
That’s because tools like ggtree are for visualising, not calculating, trees.
Is there any particular reason you want to calculate the tree in R? Most of the best tools are standalone programs.