Demography

Mathematics

Biology

Evolutionary biology

Computer science

Sociology

Genetics

Computational biology

Population

R package

Statistics

Methods in Ecology and Evolution

Summary Partially, clonal species are common in the Tree of Life. And yet, population genetic models still mostly focus on the extremes: strictly sexual versus purely asexual reproduction. Here, we present an R package built upon genclone software including new functions and several improvements. The RClone package includes functions to handle clonal data sets, allowing (i) checking for data set reliability to discriminate multilocus genotypes ( MLG s), (ii) ascertainment of MLG and semi‐automatic determination of clonal lineages ( MLL ), (iii) genotypic richness and evenness indices calculation based on MLG s or MLL s and (iv) describing several spatial components of clonality. RClone allows the one‐shot analysis of multipopulation data sets without size limitation, suitable for data sets now increasingly produced through next‐generation sequencing. A major improvement compared to existing software is the ability to determine the threshold to cluster similar MLG s into MLL s, based on implemented simulations...

RClone: a package to identify MultiLocus Clonal Lineages and handle clonal data sets in <scp>r</scp>.

RClone: a package to identify MultiLocus Clonal Lineages and handle clonal data sets in r.