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A lightweight python library for working with trees and biological sequence collections

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Sprucing up bioinformatics analysis

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pip install picea

picea has datastructures and methods to perform common bioinformatics tasks. Currently sequences, sequence annotations, trees, and ontologies are supported.


from picea import Tree, treeplot
import matplotlib.pyplot as plt

newick = '(((a,b),(c,d)),e)'
tree = Tree.from_newick(newick)

fig, (ax1, ax2) = plt.subplots(ncols = 2, figsize = (10, 4))

#left-to-right layout with direct links
treeplot(tree, style='rectangular', ltr=True, ax=ax1)

#right-to-left layout with square links
treeplot(tree, style='square', ltr=False, ax=ax2)

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