TREETAPPER
Prepared by: gendlerk
Tool Name: TreeTapper
Homepage: http://www.treetapper.org/
Platforms: web
Purpose:
TreeTapper is a website for finding tools to better understand biology using phylogentic trees. It also identifies areas where tools are missing and in need of further development. This website is a result of Brian O'Meara's postdoc work at NESCent.
Description:
TreeTapper is a synthetic literature and software review of available methods from paleontology, phylogenetics, genomics, and related disciplines that seek to understand character evolution using phylogenies. Methods are characterized for required data (character types, topologies or trees with branch lengths, measurement of intrataxon variation or single values per taxon, etc.), input format (Nexus, etc.), method type (nonparametric, likelihood, Bayesian, etc.), means for evaluating significance/meaningfulness of results (likelihood ratio tests, information theoretic methods, Bayes factors, etc.), software platform, software license (GNU Public License, closed source, etc.), software distribution (by request only, free download, etc.), and frequency of use (measured by citations, weighted by year). Users can identify the software they need to answer questions, especially approaches from other fields.TreeTapper currently has information on 60 questions, 55 methods, 6 programs, 2,895 references, and 3,181 people.
Controlled vocabularies can be found here.
Inputs: A user selects answers to a series of questions relating to the type of analysis they would like to perform.
Outputs: A list of programs/tools that will answer the user's question.
Relevant Publications:
Related Software: TreeTapper is similar to Joe Felsenstein's site of phylogeny programs but differs in important ways. Felsenstein's site lists a wide range of programs related to phylogenetics, including tree-building programs. TreeTapper only has programs that use phylogenies to understand evolution. On the other hand, Felsenstein's site is focused just on existing programs (which are characterized by method, platform, etc.); TreeTapper includes questions and methods, even those not implemented in current software, making it much easier to find areas which still need more work.