Data for: Ancient rapid radiation explains most conflicts among gene trees and well-supported phylogenomic trees of nostocalean cyanobacteria

Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread Horizontal Gene Transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic datasets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic datasets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny..., This dataset includes the draft genome assemblies from 220 cyanobacterial strains, 215 of which were previously published and retrieved from Genbank (see Table S1 in the associated manuscript) and 5 generated as part of the study. It also includes all the data, code, and output files generated as part of the analyses in the paper. See the README.md for more information. Visit also the project's GitHub repository (https://github.com/cjpardodelahoz/nostocales), which contains the version history of all the code, as well as detailed workflows for the analyses conducted as part of the study. , , # Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-supported Phylogenomic Trees of Nostocalean Cyanobacteria

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This repository contains the Supplementary materials, files, as well as all the code, data and outputs from the analyses used in the study.

## Description of the data and file structure

This repository contains Supplementary Materials, code and data. See below for details of the file structure.

### Supplementary Materials

The supplementary materials are distributed in two files:

* `PardoDelaHoz_nostocales_suppl.pdf`: this is the main Supplementary Materials file. It contains all supplementary figures and tables, with captions, as well as the references.
* `Supplemtary_file_S1.csv`: this is a table that summarizes the results of the GUNC analyses.

### Code

The code distributed in two files:

* `commands.sh`: This file has the full workflow with calls to all the scripts. It is intended to be a reference to navigate the scripts.
* `scripts_and_m...