FN Archimer Export Format
PT J
TI RClone: a package to identify MultiLocus Clonal Lineages and handle clonal datasets in R
BT 
AF BAILLEUL, Diane
   STOECKEL, Solenn
   ARNAUD-HAOND, Sophie
AS 1:1,2;2:3;3:1,2;
FF 1:PDG-RBE-MARBEC-LHM;2:;3:PDG-RBE-MARBEC-LHM;
C1 IFREMER, UMR MARBEC, Stn Sete, Ave Jean Monnet,CS 30171, F-34203 Sete, France.
   Univ Montpellier, OREME Stn Marine, 2 Rue Chantiers,CC 99009, F-34200 Sete, France.
   INRA, UMR1349, Inst Genet Environm & Plant Protect, F-35650 Le Rheu, France.
C2 IFREMER, FRANCE
   UNIV MONTPELLIER, FRANCE
   INRA, FRANCE
SI SMEL SETE
   SETE
SE PDG-RBE-MARBEC-LHM
UM MARBEC
IN WOS Ifremer jusqu'en 2018
   copubli-france
   copubli-p187
   copubli-univ-france
IF 5.708
TC 80
UR https://archimer.ifremer.fr/doc/00319/43000/42507.pdf
LA English
DT Article
DE ;clonal diversity;clonal population;clonality;multilocus genotypes;multilocus lineages;software;spatial autocorrelation
AB 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 (MLGs), (ii) ascertainment of MLG and semi-automatic determination of clonal lineages (MLL), (iii) genotypic richness and evenness indices calculation based on MLGs or MLLs 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 MLGs into MLLs, based on implemented simulations of sexual events. Several functions allow data importation, conversion and exportation with adegenet, Genetix or Arlequin.   RClone is provided with two vignettes to handle analysis on one (RClone_quickmanual) or several populations (RClone_qmsevpops).
PY 2016
PD AUG
SO Methods In Ecology And Evolution
SN 2041-210X
PU Wiley-blackwell
VL 7
IS 8
UT 000382505900010
BP 966
EP 970
DI 10.1111/2041-210X.12550
ID 43000
ER

EF