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name: common-tree layout: post title: Getting a simple tree via NCBI date: 2013-02-14 author: Scott Chamberlain tags:
A problem that needs to be solved is getting the incrasingly vast phylogenetic information to folks not comfortable building their own phylogenies. Phylomatic has made this super easy for people that want plant phylogenies (at least 250 or so papers have used and cited Phylomatic in their papers) - however, there are few options for those that want phylogenies for other taxonomic groups.
One cool tool that was brought up was the Common Tree service provided by NCBI. Here's some help on the service. Unlike Phylomatic, Common Tree is purely based off of taxonomic relationships (A and B are both in the C family, so are sisters), not an actual phylogeny as Phylomatic is based on.
But how do you use Common Tree?
Get a species list
Grab the taxon list from my github account here
Go to the site
Go to the Common Tree site here
Hit the "choose file" button, then select the
species.txt file you downloaded in the first step.
Add the species list to make the tree
Then hit "add from file", and you got a "tree"
You can download the tree in a variety of formats, including a .phy file
Plot the tree on your machine
Make a tree, in R for me
# install.packages("ape") # install if you don't have ape library(ape) # Read the tree in. YOu get the tree back with alot of newlines (\n) - can easily take these out with a good text editor. tree <- read.tree(text="(Lampetra:4,((((((Umbra:4,((Lota:4,Microgadus:4)Gadiformes:4,((Culaea:4,Apeltes:4,Pungitius:4,Gasterosteus:4)Gasterosteidae:4,(Morone:4,(Ambloplites:4,Micropterus:4,Lepomis:4)Centrarchidae:4,(Sander:4,Perca:4)Percidae:4)Percoidei:4,Cottus:4)Percomorpha:4)Holacanthopterygii:4)Neognathi:4,(((Prosopium:4,Coregonus:4)Coregoninae:4,(Salvelinus:4,Salmo:4,Oncorhynchus:4)Salmoninae:4)Salmonidae:4,Osmerus:4)Protacanthopterygii:4)Euteleostei:4,(Alosa:4,(Ameiurus:4,(Catostomus:4,(Semotilus:4,Rhinichthys:4,Margariscus:4,Couesius:4,Pimephales:4,Luxilus:4,Notemigonus:4,Notropis:4,Carassius:4)Cyprinidae:4)Cypriniformes:4)Otophysi:4)Otocephala:4)Clupeocephala:4,Anguilla:4)Elopocephala:4,Acipenser:4)Actinopteri:4,Scyliorhinus:4)Gnathostomata:4)Vertebrata:4;") # stretch the branches so tips line up tree2 <- compute.brlen(tree, method = "Grafen") # Plot the tree plot(tree2, no.margin=TRUE, cex=0.7)