Monday 13 July 2015

Making a quick plot of a phylogenetic tree

I've been trying to find nice ways to make a quick plot of a phylogenetic tree.

Here are some nice ones:
- My colleague Bhavana told me about using FigTree [note to self: this is installed on the Sanger farm]
- On the ETE2 webpage, there is a very nice TreeView tool for drawing a tree, where you can just paste in  your tree, and it makes a tree picture
- On the Sanger farm, if you logged in using 'ssh -X', you can use the ETE2 command-line tool, by typing 'ete2' with a Newick tree file name, and a GUI pops up
- You can also plot a tree using a Python script that calls ETE2, for example, this script calls ETE2 and pops up a picture of the tree in a GUI (picture below): (again, for this you need to log into the Sanger farm using 'ssh -X')

import os
import sys
from ete2 import Tree

# note: this script is in python2, as ete2 is in python2

def main():

    # check the command-line arguments:
    if len(sys.argv) != 2 or os.path.exists(sys.argv[1]) == False:
        print("Usage: %s newick_file" % sys.argv[0])
    newick_file = sys.argv[1]

    # the code below is based on examples on
    # load a tree from a file. The root node is put into 't'
    t = Tree(newick_file, format=1) # format=1 means internal node names are loaded


if __name__=="__main__":


Other tools:
- My colleague Diogo also mentioned a new tool called PhyloCanvas, which he said is very fast.

- My colleage Sam Dougan mentioned Taxonium

Note to self (sorry, this is just for me!):
[To get the Newick version of a 50HG tree, for family 141670:
%  141670 es9_compara_homology_final2_75 newick ]

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