I have been using biopython 1.72 to display my phylogenetic tree files.
1)Using the function
'Phylo.draw(pars_tree, branch_labels=lambda c: c.branch_length)' to display branch lengths as well on tree, the tree displays the branch lengths as including all numbers after decimal. While I want the numbers to be truncated to two decimal places.
Following is a python method that truncates upto
"the number required" decimal places.
def truncate(n, decimals=0): multiplier = 10 ** decimals return int(n * multiplier) / multiplier truncate (12.567, 2) #Using function 12.56 #Output
Can I use such method with biopython for branch lengths?
'Phylo.draw' function opens the window which is very narrow and if the tree file is larger, all the branches are overlapped and it gets difficult to read what is written. Does anyone know any better display method?
Following is the example code, I have been using:
from Bio import Phylo from Bio.Phylo.TreeConstruction import * from Bio import AlignIO aln = AlignIO.read(open('example.phy'), 'phylip') calculator = DistanceCalculator() dm = calculator.get_distance(aln) constructor = DistanceTreeConstructor() njtree = constructor.nj(dm) starting_tree = njtree scorer = ParsimonyScorer() searcher = NNITreeSearcher(scorer) constructor = ParsimonyTreeConstructor(searcher, starting_tree) pars_tree = constructor.build_tree(aln) Phylo.draw(pars_tree, branch_labels=lambda c: c.branch_length)
I have an msa file as input and it gives a tree, which looks like:
_______ Human _______| | |_______ Chimpanzee _______| | | _______ Dog _______| |_______| | | |_______ Cow _______| | | | |_______________________ Elephant _______| | | | |_______________________________ Mouse | | _______| |_______________________________________ Platypus | | | | _______________________________________ Anole_lizard | |_______| ______| | _______________________________ Chicken | | |_______| | | |_______________________________ Zebra_finch | | | |_______________________________________________________ Xenopus _| | _______________________________________________________ Zebrafish |______| | |_______________________________________________________ Fugu | |______________________________________________________________ Amphioxus