This repository contains files and data associated with the assembly and analyses of the Opuntieae plastomes published in Köhler et al. (2023) More than a prickly morphology: plastome variation in the prickly pear cacti. Annals of Botany, 10.1093/aob/mcad098.
Edit: Figure 1 was rendered with low resolution in the paper, and is uploaded here in high resolution.
Folder 0 has data associated with the assemblies, containing (1) raw graphs (.fastg) generated by GetOrganelle, as well as the get_org.log of the samples analyzed with information regarding each of the settings for assemblies; and (2) the annotated plastomes.
Folder 1 has all the alignments analyzed in the manuscript for each data set (full_ptDNA and ptGenes) with different trimming strategies (1.Raw, 2.GBlock_NoGaps, 3.Gblock_HalfOfGaps, and 4.GBlock_AllGaps).
Folder 2 has the maximum-likelihood tree of each data set analyzed.
Folder 3 has the data and codes associated with incongruence analyses. On the root of the folder, R code for annotating intergenic-spacers; following 0.Alignments (1.Raw and 2.Gblock-NoGaps, for genes and intergenic regions); 1.geneTrees, rooted, with 0.all-bs values branches, and 1.bs-40, with branches <= 40 bs collapsed. DeltaTest folders have the R code for each of the analyses accompanied by the associated trees for the tests.