This folder contains supplementary code and data used in the inference of the phylogeny of Dryophthorinae.
Chamorro ML, de Medeiros BAS, Farrell BD. in review. First phylogenetic analysis of Dryophthorinae (Coleoptera, Curculionidae) based on structural alignment of ribosomal DNA reveals Cenozoic diversification. Ecology and Evolution
Alignment and uncalibrated Bayesian tree by M. Lourdes Chamorro and other code by Bruno A. S. de Medeiros, 2020.
This folder contains code used in the analyses
1-IQTREE: bash call to IQTREE, input alignments and partitions. MUSCLE and structural alignments in different folders.2-partitionfinder: input alignment and configuration file to PartitionFinder. MUSCLE and structural alignments in different folders.3-mrbayes: Inferences in MrBayes, including uncalibrated tree, node dating (ND) and fossilized birth-death (FBD). For the latter 2, we include scripts used to run mrbayes and also to produce summary trees. MUSCLE and structural alignments in different folders in the case of uncalibrated analyses.4-figure: R code used to produce the figure with calibrated analyses, including html file with R code and output.
This folder contains results from the analyses in the Code folder.
Results for 4-figure are included in the Rmarkdown output.
Included folders
1-IQTREE: output files from IQTREE, including tree and best partition scheme. MUSCLE and structural alignments in different folders.2-partitionfinder: output files from PartitionFinder, including best partition scheme. MUSCLE and structural alignments in different folders.3-mrbayes: Summary trees obtained from Mrbayes, including posterior distribution with 10000 trees. MUSCLE and structural alignments in different folders in the case of uncalibrated analyses.