Bio.PhyloA unified phylogenetics toolkit for Biopython

Eric Talevich

Institute of BioinformaticsUniversity of Georgia

June 29, 2010

Abstract

Bio.Phylo is a new phylogenetics library for:

• Exploring, modifying and annotating trees

• Reading & writing standard file formats

• Quick visualization

• Gluing together computational pipelines

Availability: Biopython 1.54

A quick survey of file formats

Newick (a.k.a. New Hampshire) is a simple nested-parens

format: (A, (B, C), (D, E))• Extended & tweaked, led to NHX (and parsing

problems)

Nexus is a collection of formats, including Newick trees• More than just tree data. . . still tough to parse

PhyloXML is an XML-based replacement for NHX• Annotations formalized as XML elements;

extensible with user-defined element types

NeXML is an XML-based successor to Nexus• Ontology-based — key-value assignments have

semantic meaning

Demo: What’s in a tree?

1. Read a simple Newick file

2. Inspect through IPython

3. Draw withPyLab/matplotlib

4. Promote to a PhyloXML tree

5. Set branch colors

6. Write a PhyloXML file

# In a terminal, make a simple Newick file

# Then launch the IPython interpreter and read the file

% cat > simple.dnd <<EOF

> (((A,B),(C,D)),(E,F,G))

> EOF

% ipython -pylab

>>> from Bio import Phylo

>>> tree = Phylo.read(’simple.dnd’, ’newick’)

# String representation shows the object structure

>>> print tree

Tree(weight=1.0, rooted=False, name=’’)

Clade(branch_length=1.0)

Clade(branch_length=1.0)

Clade(branch_length=1.0)

Clade(branch_length=1.0, name=’A’)

Clade(branch_length=1.0, name=’B’)

Clade(branch_length=1.0)

Clade(branch_length=1.0, name=’C’)

Clade(branch_length=1.0, name=’D’)

Clade(branch_length=1.0)

Clade(branch_length=1.0, name=’E’)

Clade(branch_length=1.0, name=’F’)

Clade(branch_length=1.0, name=’G’)

# Draw an ASCII-art dendrogram

>>> Phylo.draw_ascii(tree, column_width=52)

______________ A

______________|

| |______________ B

______________|

| | ______________ C

| |______________|

_| |______________ D

|

| ______________ E

| |

|______________|______________ F

|

|______________ G

>>> tree.rooted = True

>>> Phylo.draw graphiz(tree)

E

C

B

G

A

D

F

# Promote a basic tree to PhyloXML

>>> from Bio.Phylo.PhyloXML import Phylogeny

>>> phy = Phylogeny.from_tree(tree)

>>> print phy

Phylogeny(rooted=True, name=’’)

Clade(branch_length=1.0)

Clade(branch_length=1.0)

Clade(branch_length=1.0)

Clade(branch_length=1.0, name=’A’)

Clade(branch_length=1.0, name=’B’)

Clade(branch_length=1.0)

Clade(branch_length=1.0, name=’C’)

Clade(branch_length=1.0, name=’D’)

Clade(branch_length=1.0)

Clade(branch_length=1.0, name=’E’)

Clade(branch_length=1.0, name=’F’)

Clade(branch_length=1.0, name=’G’)

Branch color

>>> phy.root.color = (128, 128, 128)

Or:>>> phy.root.color = ’#808080’

Or:>>> phy.root.color = ’gray’

Find clades by attribute values:>>> mrca = phy.common ancestor({’name’:’E’},

{’name’:’F’})>>> mrca.color = ’salmon’

Directly index a clade:>>> phy.clade[0,1].color = ’blue’

>>> Phylo.draw graphviz(phy, prog=’neato’)

E

C

F

A

D

G

B

# Save the color annotations in phyloXML

>>> Phylo.write(phy, ’simple-color.xml’, ’phyloxml’)

<phy:phyloxml xmlns:phy="http://www.phyloxml.org">

<phylogeny rooted="true">

<clade>

<branch_length>1.0</branch_length>

<color>

<red>128</red>

<green>128</green>

<blue>128</blue>

</color>

<clade>

<branch_length>1.0</branch_length>

<clade>

<branch_length>1.0</branch_length>

<clade>

<name>A</name>

...

Thanks

Holla:

• Brad Chapman and Christian Zmasek, GSoC 2009 mentors

• The Biopython developers, feat. Peter J. A. Cock,Frank Kauff & Cymon J. Cox

• Hilmar Lapp & the NESCent Phyloinformatics program

• Google’s Open Source Programs Office

• My professor, Dr. Natarajan Kannan

• Developers like you

Q&A

• Which 3rd-party applications should we wrap inBio.Phylo.Applications? (e.g. RAxML, MrBayes)

• Which other libraries should we support interoperability with?(PyCogent, ape)

• What other algorithms are simple, stable and relevant?(Consensus, rooting)

• Features for systematics? (Geography, PopGen integration?)

Extra: Tree methods>>> dir(tree)

collapse

collapse all

common ancestor

count terminals

depths

distance

find any

find clades

find elements

get nonterminals

get path

get terminals

is bifurcating

is monophyletic

is parent of

is preterminal

ladderize

prune

split

total branch length

trace

See: http://biopython.org/DIST/docs/api/Bio.Phylo.

BaseTree.TreeMixin-class.html

Extra: The Bio.Phylo class hierarchy

Figure: Inheritance relationship among the core classes

Extra: PhyloXML classes

$ pydoc Bio.Phylo.PhyloXML

AccessionAlphabetAnnotationBaseTreeBinaryCharactersBranchColorCladeCladeRelationConfidence

DateDistributionDomainArchitectureEventsIdMolSeqOtherPhylogenyPhyloxml

PointPolygonPropertyProteinDomainReferenceSequenceSequenceRelationTaxonomyUri

See: http://biopython.org/wiki/PhyloXML