Double-digested RADseq (ddRADseq) is a NGS methodology that generates reads from thousands of loci targeted by restriction enzyme cut sites, across multiple individuals. To be statistically sound and economically optimal, a ddRADseq experiment has a preliminary design stage that needs to consider issues related to the selection of enzymes, particular features of the genome of the focal species, possible modifications to the library construction protocol, coverage needed to minimize missing data, and the potential sources of error that may impact upon the coverage. We present ddradseqtools, a software package to help ddRADseq experimental design by (i) the generation of in silico double-digested fragments; (ii) the construction of modified ddRADseq libraries using adapters with either one or two indexes and degenerate base regions (DBRs) to quantify PCR duplicates; and (iii) the initial steps of the bioinformatics preprocessing of reads. ddradseqtools generates single-end (SE) or paired-end (PE) reads that may bear SNPs and/or indels. The effect of allele dropout and PCR duplicates on coverage is also simulated. The resulting output files can be submitted to pipelines of alignment and variant calling, to allow the fine-tuning of parameters. The software was validated with specific tests for the correct operability of the program. The correspondence between in silico settings and parameters from ddRADseq in vitro experiments was assessed to provide guidelines for the reliable performance of the software. ddradseqtools is cost-efficient in terms of execution time, and can be run on computers with standard CPU and RAM configuration.
SIMHYB is a Java-based software for the simulation of mixed hybridizing populations. The program is intended for the analysis of the effect of the different demographic and adaptive parameters on the evolution of these populations. Census size of each species, number of intermediate specific classes, directional fertility among them and fitness coefficient of each class can be defined by the user. Inheritance of fitness and ageing effect are also taken into account. The software generates individuals of known pedigree, allowing their traceability throughout the generations. SIMHYB yields for each simulated generation an output file easily convertible to an input for STRUCTURE (Pritchard JK, Stephens M, Donnely P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959), one of the most popular softwares for the Bayesian analysis of populations.