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Phylocom: software for the analysis of phylogenetic community structure and trait evolution
Open accessAbstract
Motivation: The increasing availability of phylogenetic and trait data for communities of co-occurring species has created a need for software that integrates ecological and evolutionary analyses. Capabilities: Phylocom calculates numerous metrics of phylogenetic community structure and trait similarity within communities. Hypothesis testing is implemented using several null models. Within the same framework, it measures phylogenetic signal and correlated evolution for species traits. A range of utility functions allow community and phylogenetic data manipulation, tree and trait generation, and integration into scientific workflows. Availability: Open source at: http://phylodiversity.net/phylocom/ Contact: cwebb@oeb.harvard.edu
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Citations
Cites
Phylogenies and the Comparative Method
Felsenstein, J. (1985) · The American Naturalist · doi:10.1086/284325 · Cited by 9,793
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Jones, R. T., Robeson, M. S., Lauber, C. L., Hamady, M., Knight, R., & Fierer, N. (2009) · The ISME Journal · doi:10.1038/ismej.2008.127 · Cited by 1,230
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Burkle, L. A., Marlin, J. C., & Knight, T. M. (2013) · Science · doi:10.1126/science.1232728 · Cited by 1,118
Functional and phylogenetic diversity as predictors of biodiversity–ecosystem-function relationships
Flynn, D. F. B., Mirotchnick, N., Jain, M., Palmer, M. I., & Naeem, S. (2011) · Ecology · doi:10.1890/10-1245.1 · Cited by 890
Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama
Kress, W. J., Erickson, D. L., Jones, F. A., Swenson, N. G., Perez, R., Sanjur, O., & Bermingham, E. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909820106 · Cited by 722
Metadata
- Authors
- Webb, C. O., Ackerly, D. D., & Kembel, S. W.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-08-04
- Volume
- 24
- Issue
- 18
- Pages
- 2098-2100
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2164035292
- Cited by
- 1,821
- References
- 1
- FWCI
- 75.27
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Webb, C. O., Ackerly, D. D., & Kembel, S. W. (2008). Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics. https://doi.org/10.1093/bioinformatics/btn358
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