Species identity and evolution in R
Species identity and evolution in R
1. Brown et al. (2012) Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding. Molecular Ecology Resources. URL.
2. Collins et al. (2012) Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification. Methods in Ecology and Evolution. URL.
3. Collins et al. (2012) Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade. PLoS ONE. URL.
4. Boyer et al. (2012) Sliding window analyses for optimal selection of mini-barcodes, and application to 454-pyrosequencing for specimen identification from degraded DNA. PLoS One. URL.
5. Brown et al. (2012) Molecular phylogenetics of a South Pacific sap beetle species complex (Carpophilus spp., Coleoptera: Nitidulidae). Molecular Phylogenetics and Evolution. URL.
6. Herrera et al. (2012) Spatial and temporal patterns of genetic variation in the widespread antitropical deep-sea coral Paragorgia arborea. Molecular Ecology. URL.
7. Collins (2012) Investigating interspecific hybridisation in ornamental fishes. figshare. URL.
8. Van der Bank et al. (2012) DNA barcoding reveals micro-evolutionary changes and river system-level phylogeographic resolution of African silver catfish Schilbe intermedius (Actinopterygii: Siluriformes: Schilbeidae) from seven populations across different African river systems. Acta Ichthyologica et Piscatoria. URL.
9. Collins and Cruickshank (2013) The seven deadly sins of DNA barcoding. Molecular Ecology Resources. URL.
What's up
- spiderDev version 0.0-9, comprising a number of bleeding-edge functions under development for inclusion in spider is now available from R-Forge
- Spider is now published in Molecular Ecology Resources. URL.
- Spider version 1.1-5 is now available from CRAN
- Spider was presented at the 4th International Barcode Of Life Conference in Adelaide (Nov. 2011)
Download
Benchmarking ape's ability to handle large DNA alignments (Sweave file)
papers using SPIDER
1. Brown et al. (2012) Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding. Molecular Ecology Resources. URL.
LINKS
Spider summary page on R-Forge
Spider public forum on R-Forge
4th International Barcode Of Life Conference
The SPIDER Team
Sam Brown, Rupert Collins, Stephane Boyer, Rob Cruickshank, Marie-Caroline Lefort, Jagoba Malumbres-Olarte, Cor Vink...
PAPERS USING SPIDER