haotu : an open lab notebook

2011/02/14

Add taxa to phylogeny with dated branch lengths and nodes

Filed under: bladj, phylocom, phylogeny, R — S @ 14:41

This is a common problem I have when trying to construct a phylogeny for a set of taxa when all taxa do not have sequence data associated.

1. read your tree into R as a phylo object

2a. label all the nodes

tree<-makeNodeLabel(tree)

2b. your tree may not have branch lengths and thus no branching times (which you need in the next step), so add arbitrary branch lengths to your tree.

tree<-compute.brlen(tree)

3.  output the node dates and put them in a spreadsheet program like excel

t(t(branching.times(tree)))

4. remove the branch lengths (or if you have a the original tree without branch lengths just use that)

compute.brlen(tree,method=1)->tree
write.tree(tree)

copy the output into a text editor and remove all occurrences of :1

5. add your taxa to the newick formatted phylogeny that is in your text editor. Add them where you hypothesize they should be. Also name the nodes as you go and add them to your list of nodes that you copied to excel. This may take some time.

6. Then use phylocom and the bladj function to date those added nodes. I typically start with the timetree of life website to find dates for the nodes: http://www.timetree.org/

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