1. CIPRES Software architecture/development Focus Leader: Mark Holder (FSU) Architecture:Wayne Maddison (UBC) Mark Holder (FSU) David Swofford (FSU) Implementation: Project manager: Mark Miller (SDSC) Chief programmers: Mark Holder (FSU) Terri (Liebowitz) Schwartz (SDSC) Other programmers: Alex Borchers (SDSC) Zhijie Guan (SDSC) Tim McPhillips (SCSC) Other contributors: Paul Lewis (UConn), Yu Fan (UConn), David Maddison (Arizona), Peter Midford (UBC), Rutger Vos (UBC), Tandy Warnow (UT), Bernard Moret (UNM)

2. The Grand Goal: Phylogeny of all Life www.tolweb.org

3. The Individual Goal: Phylogeny of My Group

4. The Grand Goal will be achieved by combining efforts

5. Combining data: Supermatrices

6. The Grand Goal will be achieved by combining efforts Combining data: Supermatrices Combining results: Supertrees

7. The Grand Goal will be achieved by combining efforts Combining data: Supermatrices Combining results: Supertrees Combining programming: Supertools

8. As data grow, computational demand grows Problem 1: How to make analytical tools that can handle trees of 100,000 taxa X 100,000 characters?

9. Solution?: Hire 25 programmers to write the Monster App For Phylogenetics No: A short term strategy. Better to build a foundation that will enable a worldwide community of programmers to contribute

10. Solution?: Change our mode of software development Current analytical tools: PAUP*, MrBayes, PHYLIP, TNT: ≤ 3 authors Future analytical tools: Need community programming, with shared effort and rapid incorporation of new algorithmic ideas

11. The workflow of a phylogenetic study involves many data, many analyses, many results Problem 2: How to manage information?

12. Habronattus Pellenes Bianor Plexippus... Samples Preservation Sequencin g Alignment tissues aligned sequences Tree inference —choice of method —model inference —search strategy Implications of trees — character evolution — speciation/extinction — coevolution Phenotypic observation sequences Coding matrix data matrix Publish ! Data storage (e.g. NEXUS, database) Tree storage (e.g, NEXUS, database) trees Clustal, etc. Sequencher, etc. PAUP*, MrBayes, PHYLIP, TNT, etc. Discrete, MacClade, Mesquite, etc. Workflow for phylogenetic analysis

13. Habronattus Pellenes Bianor Plexippus... Samples Preservation Sequencin g Alignment tissues aligned sequences Genbank Tree inference —choice of method —model inference —search strategy Implications of trees — character evolution — speciation/extinction — coevolution trees Databases Phenotypic observation sequences Coding matrix data matrix Specimen database Publish ! TreeBASE Data storage (e.g. NEXUS, database) Tree storage (e.g, NEXUS, database) matrix

14. Habronattus Pellenes Bianor Plexippus... Samples Preservation Sequencin g Alignment tissues aligned sequences Genbank Tree inference —choice of method —model inference —search strategy Implications of trees — character evolution — speciation/extinction — coevolution trees Information transfer Phenotypic observation sequences Coding matrix data matrix Specimen database Publish ! TreeBASE Data storage (e.g. NEXUS, database) Tree storage (e.g, NEXUS, database) matrix

15. Footnote Programs serve so many functions, CIPRES can't possibly make major improvements for all of these software needs

16. Solutions for information management A communications infrastructure can mediate information transfer between programs Databases can store data, methods, results

17. CIPRES architecture, first goal: to build a communications infrastructure Modules (programs) communicate data, commands and results Modules depend on each other for services Modules can be on different machines, in different languages

18. CIPRES modular architecture Tree improver Tree evaluator Coordinator Tree decomposer Tree Merger Front End DCM (highly simplified)

19. Why start by building a modular system (i.e., a communications infrastructure)? — handles information transfer among modules — provides flexibility of analysis — facilitates quick implementation of new algorithms — facilitates distributed processing — via API, defines a common language of phylogenetic communication — engages/creates broad community of programmers

20. CIPRES Communication Tree improver Tree evaluator Coordinator Tree decomposer Tree Merger Front End multi-platform multi-language GUI command translation snapshotting error handling logging

21. And how far have we come, exactly?