Data from: A densely sampled nuclear phylogenomic analysis of the coryphoid palms (Arecaceae − Coryphoideae)

Data from:

Wrisberg, O, Petoe, P, de Lima Ferreira, P, Bacon, CD, Barfod, AS, Bellot, S, Cano, Á, Couvreur, TLP, Dransfield, J, Henderson, A, Stauffer, F, Baker, WJ, Eiserhardt, WL (in review) A densely sampled nuclear phylogenomic analysis of the coryphoid palms (Arecaceae − Coryphoideae)

This repository is meant to provide the most important data outputs produced by the Pipeline created for this project. The analysis pipeline is located on github (https://github.com/pebgroup/coryphoideae_species_tree). Raw data can be found on the NCBI Sequence Read Archive. 

The data folder is divided into the following subfolders:

01_unaligned_sequences_per_specimen

This folder contains the unaligned sequences for each specimen. The sequences are named after the specimen number.

02_unaligned_sequences_per_gene

This folder contains the unaligned sequences for each gene. The sequences are named after the gene name.

03_aligned_sequences_per_gene

This folder contains the sequences aligned by MAFFT for each gene. The sequences are named after the gene name.

04_gene_trees

This folder contains the gene trees for each gene. The trees are named after the gene name. The subfolder subset_single_copy_gene_trees contains copies of the gene trees for the single copy genes.

05_species_trees

This folder contains the species trees. The subfolder all_genes contains the species trees based on all genes, while the subfolder single_copy_genes contains only the species trees based on the single copy genes.

06_supporting_information

This folder contains a list which contains the associations between tip names and specimen numbers and a list of the single-copy genes.