exon capture phylogenomics, data and workflows (dryad_34274)

Data and computational workflows to accompany "Exon capture phylogenomics: efficacy across scales of divergence," by Jason Bragg, Sally Potter, Ke Bi and Craig Moritz

concatenated dataset used for RAxML analysis

Concatenated alignment of the complete dataset (1361 loci) and the inferred maximum likelihood RAxML tree (100 tree searches, 1000 bootstrap replicates

Alignments

All 1852 loci (contains both complete and incomplete, up to 1 species missing, alignments

Supplementary figures

Supplementary figures in order and as described in manuscrip

ASTRAL incomplete dataset, ranked locus subsets

The ASTRAL input and output for the summary-coalescent species tree analysis based on the complete dataset. Locus subsets were ranked (i.e. ranked by Tree Certainty score) selected

ASTRAL incomplete dataset, random locus subsets

The ASTRAL input and output for the summary-coalescent species tree analysis based on the incomplete dataset. Locus subsets were randomly (i.e. not ranked by Tree Certainty score) selected

Supplementary_Table_1

Information on individuals used in the study and sequencing succes

ASTRAL complete dataset, random locus subsets

The ASTRAL input and output for the summary-coalescent species tree analysis based on the complete dataset. Locus subsets were randomly (i.e. not ranked by Tree Certainty score) selected

ASTRAL complete dataset, ranked locus subsets

The ASTRAL input and output for the summary-coalescent species tree analysis based on the complete dataset. Locus subsets were ranked (i.e. ranked by Tree Certainty score) selected

Nicotra et al MEC data archive part 1

Data from phenotype analyses, crossing and autogamy experiments as well as herbarium accession data