tree = PhyloTree('(Orangutan,Human,Chimp);') tree.link_to_alignment(""" >Chimp HARWLNEKLRCELRTLKKLGLDGYKAVSQYVKGRA >Orangutan DARWINEKLRCVSRTLKKLGLDGYKGVSQYVKGRP >Human DARWHNVKLRCELRTLKKLGLVGFKAVSQFVIRRA """) nt_sequences = {"Human" : "GACGCACGGTGGCACAACGTAAAATTAAGATGTGAATTGAGAACTCTGAAAAAATTGGGACTGGTCGGCTTCAAGGCAGTAAGTCAATTCGTAATACGTCGTGCG", "Chimp" : "CACGCCCGATGGCTCAACGAAAAGTTAAGATGCGAATTGAGAACTCTGAAAAAATTGGGACTGGACGGCTACAAGGCAGTAAGTCAGTACGTTAAAGGTCGTGCG", "Orangutan": "GATGCACGCTGGATCAACGAAAAGTTAAGATGCGTATCGAGAACTCTGAAAAAATTGGGACTGGACGGCTACAAGGGAGTAAGTCAATACGTTAAAGGTCGTCCG" } for l in nt_sequences: (tree & l).nt_sequence = nt_sequences[l] tree.dist = 0 ts = TreeStyle() ts.title.add_face(TextFace("Example for nucleotides...", fsize=15), column=0) ts.layout_fn = test_layout_evol tree.show(tree_style=ts) # Show very large algs tree = PhyloTree('(Orangutan,Human,Chimp);') tree.link_to_alignment(">Human\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)]) + \ "\n>Chimp\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)]) + \ "\n>Orangutan\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)])) tree.dist = 0 ts = TreeStyle() ts.title.add_face(TextFace("better not set interactivity if alg is very large", fsize=15), column=0) ts.layout_fn = test_layout_phylo_aa