RADIS: analysis of RAD-seq data for interspecific phylogeny.
In an attempt to make the processing of RAD-seq data easier and allow rapid and automated exploration of parameters/data for phylogenetic inference, we introduce the perl pipeline RADIS Users of RADIS can let their raw Illumina data be processed up to phylogenetic tree inference, or stop (and restart) the process at some point. Different values for key parameters can be explored in a single analysis (e.g. loci building, sample/loci selection), making possible a thorough exploration of data. RADIS relies on Stacks for demultiplexing of data, removing PCR duplicates and building individual and catalog loci. Scripts have been specifically written for trimming of reads and loci/sample selection. Finally, RAxML is used for phylogenetic inferences, though other software may be utilized.



RADIS is written in perl, designed to run on Linux and Unix platforms. RADIS and its manual are freely available from http://www1.montpellier.inra.fr/CBGP/software/RADIS/.



astrid.cruaud@supagro.inra.fr



Supplementary data are available at Bioinformatics online.
INRA, UMR1062 CBGP, F-34988 Montferrier-sur-Lez, France.
Astrid
A
Cruaud
INRA, UMR1062 CBGP, F-34988 Montferrier-sur-Lez, France, IBC, F-34095 Montpellier, France.
Mathieu
M
Gautier
INRA, UMR1062 CBGP, F-34988 Montferrier-sur-Lez, France.
Jean-Pierre
JP
Rossi
INRA, UMR1062 CBGP, F-34988 Montferrier-sur-Lez, France.
Jean-Yves
JY
Rasplus
INRA, UMR441 LIPM, F31326 Castanet Tolosan, France CNRS, UMR2594 LIPM, F31326 Castanet Tolosan, France.
Jérôme
J
Gouzy
D010802:Phylogeny; D017421:Sequence Analysis; D012984:Software