Christian M Zmasek, PhDBurnham Institute for Medical Research

Bioinformatics and Systems Biologywww.phylosoft.orgwww.phyloxml.org

PhylogenomicsOriginal definition

the application of phylogenetic information for gene function analysis (Eisen, 1998)

Recent usagespecies evolution based on whole genome

analyses (for example, Dunn et al., 2008)various types of studies at the intersection of

genomics and phylogenetics

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RAT

MOUSE

HUMAN

CIONA

RAT

CIONA

MOUSE

HUMANCIONA

RAT

CIONA

Y

Z

: query sequence

: orthologous to query

: most similar to query

: gene duplication

RAT

X

Z

Y

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What information do we need for a phylogenomic analysis (sequence function analysis type)?In phylogenomic analyzes, tree nodes might

be annotated with:Sequence nameSpecies nameDuplication: true/false

Branches might be annotated with:Branch lengthsSupport values (bootstrap, probability, …)

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What information might we need for other types of phylogenomic analyses?Support values (possible multiple)Taxonomy information (possibly detailed)Geographic informationHost/parasite data (relation between tree

nodes)Gene expression valuesGenomic locationMutations, variation, disease…

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How is this information processed and stored?Tree topologies are described by hierarchical parenthesis:

((A,B),C)Unique tree node labels mapped to text files, spreadsheets,

databasesManual processing of text files with text editorsMacros, shell scripts, Perl scriptsNew Hamphshire eXtended (NHX) format

Adds tags for different fields: Species: S= Bootstrap support: B=

Example: ADH2:0.1[&&NHX:S=human:B=90]http://www.phylosoft.org/forester/NHX.html

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How is this information published?Mostly as images of phylogenetic trees in

journalsnot suitable as input for further studies!

Submission to (publicly accessible) databases rare

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Problems with this approachTediousError pronePublished images are difficult to use as input

for further studiesMeta-analyzes are hardDifferent, and incompatible, “dialects” of

NHX appearedLimited expressiveness

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phyloXML by example<phylogeny rooted="true"> <name> example from Prof. Joe Felsenstein's book "Inferring Phylogenies“ </name> <clade> <clade> <branch_length>0.06</branch_length> <clade> <name>A</name> <branch_length>0.102</branch_length> </clade> <clade> <name>B</name> <branch_length>0.23</branch_length> </clade> </clade> <clade> <name>C</name> <branch_length>0.4</branch_length> </clade> </clade></phylogeny>

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phyloXMLImportant elements:

TaxonomySequenceConfidenceEvents (duplication, speciation)Property (“custom data”)Typed relations (between clades, sequences)

XSD schema, examples, description, applications: http://www.phyloxml.org/

Current version: 1.o

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Important clade level elements <taxonomy>

<id source=“”> <scientific_name> <common_name> <rank> <uri>

<sequence> <symbol> <accession source=“”> <name> <uri>

<confidence type=“”> <distribution>

<desc> <point geodetic_datum=“”>

<lat> <long> <alt>

<property ref=“” unit=“” datatype=“”>

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phyloXML applications/implementations (examples)BioPerl:

Parser, writerATV — A Tree Viewer

Java based tree display tool suitable for large (>10 000) and highly decorated phylogenetic/taxonomic trees

http://www.phylosoft.org/atvphyloxml_converter

Command line tool to convert Newick (NH), NHX, and Nexus formatted trees to phyloXML

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