Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES

Current genome sequencing initiatives across a wide range of life forms offer significant potential to enhance our understanding of evolutionary relationships and support transformative biological and medical applications. Species trees play a central role in many of these applications; however, despite the widespread availability of genome assemblies, accurate inference of species trees remains challenging for many scientists due to the limited automation, significant domain expertise, and substantial computational resources required by conventional methods. To address this limitation, we present ROADIES, a fully-automated pipeline to infer species trees starting from raw genome assemblies (those lacking prior annotations). In contrast to the prominent approach, ROADIES randomly selects segments of the input genomes to generate gene trees. This eliminates the need to choose any single reference species or perform the cumbersome steps of gene annotations and whole genome alignments. ROA..., , , # Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES

## Usage Notes

[https://doi.org/10.5061/dryad.tht76hf73](https://doi.org/10.5061/dryad.tht76hf73)

ROADIES is a novel pipeline designed for phylogenetic tree inference of the species directly from their raw genomic assemblies.

For further details related to how to run the tool ROADIES, please refer to our Wiki: [https://turakhia.ucsd.edu/ROADIES/](https://turakhia.ucsd.edu/ROADIES/)

This repository contains the output files generated by ROADIES (v0.1.0) ([https://github.com/TurakhiaLab/ROADIES/releases/tag/v0.1.0](https://github.com/TurakhiaLab/ROADIES/releases/tag/v0.1.0)) for estimating the species tree for the following datasets (in the accurate mode of operation):

* 240 mammalian species from the infraclass Placentalia (alternatively referred to as “placental mammals”)
* 100 flies species belonging to the subfamily of Drosophilinae and Steganinae
* 363 bird species from...