Fu CN, Mo ZQ, Yang JB, Cai J, Ye LJ, Zou JY, Qin HT, Zheng W, Hollingsworth PM, Li DZ, Gao LM. Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron. Molecular Ecology Resources. doi:10.1111/1755-0998.13479.



1. Files within ML_trees.zip

 File List:
   ML_trees
      ├── Dataset-A_Plastome.tre
      ├── Dataset-B_Plastome_with_no_missing.tre
      ├── Dataset-C_matK+rbcL+psbA-trnH.tre
      ├── Dataset-D_nrDNA_(3S_region).tre
      ├── Dataset-E_ITS.tre
      ├── Dataset-F_ITS+matK+psbA-trnH.tre
      ├── Dataset-G_ITS+matK+rbcL+psbA-trnH.tre
      ├── Dataset-H_Plastome+nrDNA.tre


 File descriptions: 
   Dataset-A_Plastome.tre – Tree file in newick format of Plasome.
   Dataset-B_Plastome_with_no_missing.tre – Tree file in newick format of plastome with no missing data.
   Dataset-C_matK+rbcL+psbA-trnH.tre  – Tree file in newick format of the combination of matK + rbcL + trnH-psbA.
   Dataset-D_nrDNA_(3S_region).tre – Tree file in newick format of nrDNA (18S, ITS1, 5.8S, ITS2, 26S).
   Dataset-E_ITS.tre – Tree file in newick format of ITS (ITS1-5.8S-ITS2).
   Dataset-F_ITS+matK+psbA-trnH.tre – Tree file in newick format of the combination of ITS + matK + trnH-psbA.
   Dataset-G_ITS+matK+rbcL+psbA-trnH.tre – Tree file in newick format of the combination of ITS + matK + rbcL + trnH-psbA.
   Dataset-H_Plastome+nrDNA.tre – Tree file in newick format of the combination of plasome + nrDNA.


2. Files within Sequence_alignments.zip

 File List:
   Sequence_alignments
      ├── 3S.fa
      ├── accD.fa
      ├── atpA-atpF.fa
      ├── atpA-psbI.fa
      ├── atpA.fa
      ├── atpB-rbcL.fa
      ├── atpB.fa
      ├── atpE.fa
      ├── atpF-atpH.fa
      ├── atpF-intron.fa
      ├── atpF.fa
      ├── atpH-atpI.fa
      ├── atpH.fa
      ├── atpI-rps2.fa
      ├── atpI.fa
      ├── ccsA-ndhD.fa
      ├── ccsA-rpl32.fa
      ├── ccsA.fa
      ├── cemA-petA.fa
      ├── cemA-ycf4.fa
      ├── cemA.fa
      ├── infA-rpl36.fa
      ├── infA-rps8.fa
      ├── infA.fa
      ├── matK-psbA.fa
      ├── matK.fa
      ├── ndhA-intron.fa
      ├── ndhA-ndhI.fa
      ├── ndhA.fa
      ├── ndhB-intron.fa
      ├── ndhB-rpl23.fa
      ├── ndhB-rps7.fa
      ├── ndhB.fa
      ├── ndhC-ndhK.fa
      ├── ndhC-rbcL.fa
      ├── ndhC.fa
      ├── ndhD-psaC.fa
      ├── ndhD.fa
      ├── ndhE-ndhG.fa
      ├── ndhE-psaC.fa
      ├── ndhE.fa
      ├── ndhF.fa
      ├── ndhG-petA.fa
      ├── ndhG.fa
      ├── ndhH-rps15.fa
      ├── ndhH.fa
      ├── ndhI.fa
      ├── ndhJ-ndhK.fa
      ├── ndhJ-rps4.fa
      ├── ndhJ.fa
      ├── ndhK.fa
      ├── petA.fa
      ├── petG-petL.fa
      ├── petG-psaJ.fa
      ├── petG.fa
      ├── petL-psbE.fa
      ├── petL.fa
      ├── petN-psbM.fa
      ├── petN.fa
      ├── psaA-psaB.fa
      ├── psaA-psbK.fa
      ├── psaA.fa
      ├── psaB-rps14.fa
      ├── psaB.fa
      ├── psaC.fa
      ├── psaI-ycf4.fa
      ├── psaI.fa
      ├── psaJ-rpl33.fa
      ├── psaJ.fa
      ├── psbA.fa
      ├── psbB-psbT.fa
      ├── psbB.fa
      ├── psbC-psbZ.fa
      ├── psbC.fa
      ├── psbD.fa
      ├── psbE-psbF.fa
      ├── psbE.fa
      ├── psbF-psbL.fa
      ├── psbF.fa
      ├── psbH-psbN.fa
      ├── psbH.fa
      ├── psbI-psbK.fa
      ├── psbI.fa
      ├── psbJ-psbL.fa
      ├── psbJ.fa
      ├── psbK.fa
      ├── psbL.fa
      ├── psbM.fa
      ├── psbN-psbT.fa
      ├── psbN.fa
      ├── psbT.fa
      ├── psbZ-rps14.fa
      ├── psbZ.fa
      ├── rbcL.fa
      ├── rpl14-rps8.fa
      ├── rpl14.fa
      ├── rpl2-rpl23.fa
      ├── rpl2-rps19.fa
      ├── rpl2.fa
      ├── rpl20-rps18.fa
      ├── rpl20.fa
      ├── rpl22-rps19.fa
      ├── rpl22.fa
      ├── rpl23.fa
      ├── rpl32.fa
      ├── rpl33-rps18.fa
      ├── rpl33.fa
      ├── rpl36-rps11.fa
      ├── rpl36.fa
      ├── rpoA-rps11.fa
      ├── rpoA.fa
      ├── rpoB.fa
      ├── rpoC1-rpoC2.fa
      ├── rpoC1.fa
      ├── rpoC2-rps2.fa
      ├── rpoC2.fa
      ├── rps11.fa
      ├── rps14.fa
      ├── rps15-rrn5.fa
      ├── rps15.fa
      ├── rps16-intron.fa
      ├── rps16.fa
      ├── rps18.fa
      ├── rps19.fa
      ├── rps2.fa
      ├── rps3.fa
      ├── rps4-ycf3.fa
      ├── rps4.fa
      ├── rps7.fa
      ├── rps8.fa
      ├── rrn16-rrn23.fa
      ├── rrn16.fa
      ├── rrn23-rrn4.5.fa
      ├── rrn23.fa
      ├── rrn4.5-rrn5.fa
      ├── rrn4.5.fa
      ├── rrn5.fa
      ├── ycf3-intron1.fa
      ├── ycf3-intron2.fa
      ├── ycf3.fa
      ├── ycf4.fa
      ├── Dataset-A_Plastome.fa
      ├── Dataset-B_Plastome_with_no_missing.fa
      ├── Dataset-C_matK+rbcL+psbA-trnH.fa
      ├── Dataset-D_nrDNA_(3S_region).fa
      ├── Dataset-E_ITS.fa
      ├── Dataset-F_ITS+matK+psbA-trnH.fa
      ├── Dataset-G_ITS+matK+rbcL+psbA-trnH.fa
      ├── Dataset-H_Plastome+nrDNA.fa


 File descriptions: 
   3S.fa – Alignment from nrDNA (18S, ITS1, 5.8S, ITS2, 26S).
   accD.fa~ycf4.fa – Alignments from coding genes, rRNA genes and intergenic regions.
   Dataset-A_Plastome.fa – The concatenated alignment file of coding genes, rRNA genes and intergenic regions of the plastid genome.
   Dataset-B_Plastome_with_no_missing.fa – The concatenated alignment file of the plastid genome data from Dataset A but using only data recovered from all samples (i.e. regions with missing data in Dataset A are removed in Dataset B).
   Dataset-C_matK+rbcL+psbA-trnH.fa – The concatenated alignment file of matK, rbcL, and trnH-psbA.
   Dataset-D_nrDNA_(3S_region).fa – Alignment from nrDNA.
   Dataset-E_ITS.fa – Alignment from ITS (ITS1-5.8S-ITS2).
   Dataset-F_ITS+matK+psbA-trnH.fa – The concatenated alignment file of ITS, matK, and trnH-psbA.
   Dataset-G_ITS+matK+rbcL+psbA-trnH.fa – The concatenated alignment file of ITS, matK, rbcL, and trnH-psbA.
   Dataset-H_Plastome+nrDNA.fa – The concatenated alignment file of Dataset A and Dataset D.