Analysis of RAD-seq data for InterSpecific phylogeny

In an attempt to make easier and standardize the processing of RAD-seq data for phylogenetic inference, while allowing fast and automated exploration of key analytical options, we designed the user friendly perl pipeline RADIS.
RADIS is designed to run on Linux and Unix platforms and freely available from this website.

The processing of raw data has been split up into two steps: data cleaning and data analysis.
Users can choose i) to let their raw Illumina data be processed up to phylogenetic tree inference (RADIS.pl)
ii) to perform only data cleaning (RADIS_step1_data_cleaning.pl)
iii) to perform only data analysis (RADIS_step2_data_analysis.pl)

Last version of Stacks tested for compatibility : Stacks-1.32

Last version of RAxML tested for compatibility : RAxML-8.2.4

If you use RADIS, please cite external programs used by the pipeline. Many thanks!
Suggested citation: "Analyses were performed using the Perl pipeline RADIS (Cruaud et al., 2016) that relies on Stacks (Catchen et al. 2011, 2013) for demultiplexing of data, removing PCR duplicates and building individual and catalog loci and RAxML (Statmatakis, 2006 a, b) for phylogenetic inferences".

Catchen J., Amores A., Hohenlohe P., Cresko W., Postlethwait J. 2011. Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1 : 171-182.
Catchen J., Hohenlohe P.A., Bassham S., Amores A., Cresko W.A. 2013. Stacks: an analysis tool set for population genomics. Molecular Ecology, 22 : 3124-3140.
Cruaud A.*, Gautier M.* (eq. contributors), Rossi J.-P, Rasplus J.-Y, Gouzy J. (submitted). RADIS: Analysis of RAD-seq data for InterSpecific phylogeny. Bioinformatics [PDF]
Stamatakis A. 2006a. Phylogenetic models of rate heterogeneity: A High Performance Computing Perspective. International Parallel and Distributed Processing Symposium (IPDPS 2006), Rhodes Island, Greece, 8 pp.
Stamatakis A. 2006b. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22 : 2688-2690.