PHYLOGENY AND COMPARATIVE METHODS SYMBIOMICS WORKSHOP

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1 PHYLOGENY AND COMPARATIVE METHODS SYMBIOMICS WORKSHOP March 4-7, 2013 Valencia, Spain Parc Cientific of the University of Valencia

2 Goals The aim of this workshop is to provide the attendees with a broad set of skills and knowledge in the most representative methods and tools to date available for both phylogenetic inference and comparative analysis Date and place The workshop will take place March 4-7, 2013 in Valencia (Spain) at the Parc Cientific of the Universitat de València. Classes and tutorials will run every day from 10 am until 8 pm. Chairs Martin Embley (Newcastle University) Andres Moya (Genomics and Health Area, Centre for Public Health Research (CSISP), Conselleria de Sanitat and Institute Cavanilles University of Valencia) Programme committee Peter Foster (Natural History Museum London) Mark Wilkinson (Natural History Museum London) Tom Williams (Newcastle University) Daniela Bezemer (HIV monitoring) Toni Gabaldon (Centre de Regulación Genómica) Jorg Peplies (Ribocon) Diego Santos (Institut Cavanilles) Mariana Reyes (Institut Cavanilles) Alejandro Manzano (Institut Cavanilles) Ricardo Futami (Biotechvana) Carlos Llorens (Biotechvana)

3 Registration Deadline closed Accommodation Your travel to Valencia and back home has to be booked by yourself and paid from your Symbiomics funding (or by your own if you are external attendee). Same for your accommodation but we will assist you with hotel reservation and detailed travel information. Local Organizers If you have any doubt or difficulty, feel free to contact Carlos Llorens or Laura Dominguez-Escribà, via the and phone numbers below. Phone: Phone

4 Content and topics The topics to be covered in the lectures will be: Introduction to molecular evolution Methods for sequence alignment Methods of phylogenetic reconstruction (parsimony, neighbor joining, maximum likelihood, Bayesian inference) Phylogenomics and comparative genomics Supertrees Editing and managing large trees Biogeography/phylogeography Networks Tutorials will be conducted to allow the workshop members to get familiar with the distinct software packages that will be used to analyze and/or process the data in the course of the workshop. Among the distinct software and databases that will be used are: ClustalX, Clustal W, T-Coffee, Muscle, MAFFT, SeaView, Jalview, Genedoc (creation of multiple alignments and manual refinement) MrBayes, RAxML, CLustal X, Mega ( phylogenetic inference) Phylograph (tree editing and management) ARB (package for phylogenetic data analysis) Silva Gypsy Database (GyDB) PhylomeDB

5 Workshop programme Monday, March 4 8:30-9:00 Registration 9:00-9:40 Welcome: Andres Moya Place: Salón de Actos, Vivero Empresarial Parc Cientific Lecture: Martin Embley 9:45-10:45 Introduction to the phylogenetic reconstruction analysis 10:45-11:00 Coffee break Place: Salón de Actos, Vivero Empresarial Parc Cientific 11:00-12:00 Lecture: Peter Foster Bayesian and likelihood methods of phylogenetic reconstruction. Part 1. Place: Salón de Actos, Vivero Empresarial Parc Cientific 12:00-13:00 Lecture: Peter Foster Bayesian and likelihood methods of phylogenetic reconstruction. Part 2. Place: Salón de Actos, Vivero Empresarial Parc Cientific 13:00-15:00 Lunch (Cafeteria Parc Cientific) 15:00-17:00 Training Session: Carlos Llorens and Ricardo Futami Creation and refinement of protein multiple alignments: dealing with low and fast evolving sequences using the reverse transcriptase as case study 17: Coffee Break 17:30-19:30 Training Session: Carlos LLorens and Ricardo Futami Interpreting and managing large phylogenetic trees and how to edit them for publication

6 Tuesday, March 5 Lecture: Mark Wilkinson 9:00-10:45 An introduction to the essentials of parsimony and neighbor joining methods of phylogenetic reconstruction Place: Salón de Actos, Vivero Empresarial Parc Cientific 10:45-11:00 Coffee break 11:00-13:00 Lecture: Daniela Bezemer The phylogenetic approach as a tool for epidemiology diagnosis and control: HIV-1 transmission networks among men having sex with men as case study Place: Salón de Actos, Vivero Empresarial Parc Cientific 13:00-15:00 Lunch (Cafeteria Parc Cientific) Training Session: Peter Foster and Tom Williams 15:00-17:00 Inferring Bayesian and maximum likelihood phylogenetic trees: Part 1 17:00-17:30 Coffee Break 17:30-19:00 Training Session: Peter Foster and Tom Williams Inferring Bayesian and maximum likelihood phylogenetic trees: Part 2 20:30-22:00 *Dinner at Pepita y Pulgarcita Restaurant (closet o IBIS) * This dinner is covered by the organization (you do not need to pay)

7 Wednesday, March 6 9:00-10:45 Lecture: Jorg Peplies SILVA and ARB: Databases and software for rrna gene based phylogeny and in-depth sequence analysis 10:45-11:00 Coffee break 11:00-13:00 Training Session: Jorg Peplies and Tom Williams Introduction of the ARB software package and integration of the SILVA web resource. Quality issues in public databases. 13:00-15:00 Lunch (Cafeteria Parc Cientific) 15:00-17:00 Training Session: Jorg Peplies and Tom Williams rrna gene alignments in ARB and their impact on phylogenetic reconstruction. 17:00-17:30 Coffee Break 17:30-19:00 Training Session: Jorg Peplies and Tom Williams Reconstruction and comparison of phylogenetic trees in ARB. Probe/primer Design/evaluation in ARB (if of interest). At night Free Time to getting some fun while knowing Valencia (up to you)

8 Thursday, March 7 10:45-12:30 Lecture: Toni Gabaldon Analysis of large-scale phylogenetic datasets, and inference of orthology and paralogy 12:30-14:00 Training Session: Toni Gabaldon and Tom Williams On Phylogenomics and comparative genomics (part 1) 14:00-15:30 Paella Experience * 15:30-17:00 Training Session: Toni Gabaldon and Tom Williams On Phylogenomics and comparative genomics (Part 2) 17:00-17:30 Coffee Break 17:30-19:15 Lecture: Martin Embley Research seminar on phylogenetic: Use of phylogenetic methods to understand early eukaryotic evolution 19:15-20:00 Closing Session: Andres Moya Martin Embley and every body Conclusions and interactive discussion of the issue * We take this term ( Paella Experience ) borrowed from the web which offers a learning experience in how to make a Paella according to the most canonical Mediterranean cooking style.

9 Getting there The course will take place at Vivero Empresarial, Parc Cientific Universitat de València C/ Catedrático Agustín Escardino, nº Paterna Valencia If you are hosted at IBIS hotel, you can get the Scientific Park (in native language Parc Cientific) easily taking the metro (subway) to Mas Rosari. You have a subway station close to IBIS at the 16 avinguda de les Corts Valencianes facing the Wellness Center.

10 It is quite easy, just follow the line traced in red. Enter this station and take the subway to The Empalme where you should to get off the subway and then to take the Tranvia towards Mas Rosari (after Canal 9) which is a small node of the tranvia called Santa Gemma-Parc Cientific which is the station node of destination. Here you have a schema of the tranvia network to the empalme to Santa Gemma-Parc Cientific.

11 Here you have a screenshot of Santa Gemma-Parc Cientific node When arriving there you must walk a bit (it is just a few meters do not worry) following the red line I tracebelow until arriving to the Socialnest Building which where we are.

12 Here you a have a capture of the entrance hall of the Vivero where the course will take place. This is how the entrance looks like..

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