Course on quantitative cladistics and use of TNT - 2nd Edition

January 12, 2015
INSTRUCTORS:
Dr. Goloboff and Dr. Szumik (Conicet, Argentina).

DATE: 

June 29 - July 3, 2015.

PLACE:
Facilities of the Centre de Restauració i Interpretació Paleontologica, Els Hostalets de Pierola, Barcelona (Spain).

WEBPAGE: 

http://www.transmittingscience.org/courses/phylo/cladistics/ 

PROGRAM:
- Intro and Basics. Parsimony and phylogenetic systematics. Character optimisation and mapping. Most parsimonious reconstructions and specific changes. Input/output in TNT. Dataset formats. Using GB->TNT to create matrices. Instruction files. Options for graphic output (SVG, metafiles). Creation of “batch” files. Editing trees. Handling tree files. Groups of trees, characters and taxa.
- Tree calculation. Tree searches. Exact solutions, Wagner trees, branch-swapping. Local and global optima. Use of multiple addition sequences. Improving search strategies. Factors which affect the efficiency of tree-searches. Constraints and “timeouts”.
- Ambiguity and consensus; summarizing results. Zero-length branches and collapsing rules. Types of consensus and their use; improving consensus trees; supertrees. Pruned consensus. Comparison of tree-topologies; SPR distances.
- Character weighting. Successive and implied weighting. Auto-weighted optimization. Refining character weighting with blocks; taking into account missing entries. User-defined weighting functions.
- Group supports. Concept of group support. Bremer supports; how to calculate them; search of suboptimal trees. Problems with Bremer supports; absolute and relative Bremer support. Partitioned Bremer support and individual Bremer supports. Measures based on resampling; effect of search strategies and collapsing rules. Problems with resampling methods.
- Tree search in large and difficult data sets. Special search algorithms. Sectorial searches. Ratchet and drifting. Tree fusing. Combining different algorithms. Driven searches and stabilization of consensus.
- Scripting. Automation of decisions to go beyond simple commands. Flow control. Decisions. Expressions, user variables, and internal variables. Design of simple scripts.

This course is co-organized by Transmitting Science, the Institut Catalá de Paleontologia M. Crusafont and the Centre de Restauració i Interpretació Paleontologica. Places are limited and will be covered by strict registration order. Please feel free to distribute this information between your colleagues if you consider it appropriate.