iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees
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...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2014-01-01
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| Series: | Evolutionary Bioinformatics |
| Online Access: | https://doi.org/10.4137/EBO.S16487 |
| _version_ | 1818163319875305472 |
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| author | James A. Fordyce Premal Shah Benjamin M. Fitzpatrick |
| author_facet | James A. Fordyce Premal Shah Benjamin M. Fitzpatrick |
| author_sort | James A. Fordyce |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-11T16:47:41Z |
| format | Article |
| id | doaj.art-87b1c58c4f3247c5b3366ea87075c67f |
| institution | Directory Open Access Journal |
| issn | 1176-9343 |
| language | English |
| last_indexed | 2024-12-11T16:47:41Z |
| publishDate | 2014-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Evolutionary Bioinformatics |
| spelling | doaj.art-87b1c58c4f3247c5b3366ea87075c67f2022-12-22T00:58:10ZengSAGE PublishingEvolutionary Bioinformatics1176-93432014-01-011010.4137/EBO.S16487iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic TreesJames A. Fordyce0Premal Shah1Benjamin M. Fitzpatrick2National Institute for Mathematical and Biological Synthesis, Knoxville, TN, USA.Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.National Institute for Mathematical and Biological Synthesis, Knoxville, TN, USA.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.https://doi.org/10.4137/EBO.S16487 |
| spellingShingle | James A. Fordyce Premal Shah Benjamin M. Fitzpatrick iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees Evolutionary Bioinformatics |
| title | iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees |
| title_full | iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees |
| title_fullStr | iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees |
| title_full_unstemmed | iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees |
| title_short | iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees |
| title_sort | iterates an r package for implementing a parametric rate comparison on phylogenetic trees |
| url | https://doi.org/10.4137/EBO.S16487 |
| work_keys_str_mv | AT jamesafordyce iteratesanrpackageforimplementingaparametricratecomparisononphylogenetictrees AT premalshah iteratesanrpackageforimplementingaparametricratecomparisononphylogenetictrees AT benjaminmfitzpatrick iteratesanrpackageforimplementingaparametricratecomparisononphylogenetictrees |