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Full-Text Articles in Life Sciences
Iterates: An R Package For Implementing A Parametric Rate Comparison On Phylogenetic Trees, James A. Fordyce, Premal Shah, Benjamin M Fitzpatrick
Iterates: An R Package For Implementing A Parametric Rate Comparison On Phylogenetic Trees, James A. Fordyce, Premal Shah, Benjamin M Fitzpatrick
Faculty Publications and Other Works -- Ecology and Evolutionary Biology
Patterns of diversification rate variation detected in phylogenetic hypotheses are frequently used to infer historical, ecological, and evolutionary processes. The parametric rate comparison (PRC) is a method for detecting rate variation in trees that models branch lengths as random variables drawn from familiar statistical distributions. iteRates is a library of functions for the R statistical computing environment for implementing PRC on phylogenetic trees. Here, we describe some of the functions in iteRates for subtree identification, tree manipulation, applying the PRC and K-clades PRC analyses, and conducting a whole-tree randomization test.
Sharing And Re-Use Of Phylogenetic Trees (And Associated Data) To Facilitate Synthesis, Arlin Stoltzfus, Brian C. O'Meara, Jamie Whitacre, Ross Mounce, Emily L. Gillespie, Sudhir Kumar, Dan F. Rosauer, Rutger A. Vos
Sharing And Re-Use Of Phylogenetic Trees (And Associated Data) To Facilitate Synthesis, Arlin Stoltzfus, Brian C. O'Meara, Jamie Whitacre, Ross Mounce, Emily L. Gillespie, Sudhir Kumar, Dan F. Rosauer, Rutger A. Vos
Faculty Publications and Other Works -- Ecology and Evolutionary Biology
Background
Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote sharing of data reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing trees and associated data so as to promote re-use.
Findings
Here we summarize results of an ongoing analysis of current practices for archiving phylogenetic trees and associated data, current practices of re-use, and current barriers to re-use. We find …