v1.0.0

In this pre-release, you shall find two tutorials to run MCMCtree:

• Reproducible timetree inference: step-by-step guidelines for timetree inference with PAML under a reproducible environment. You will follow all the steps within a self-contained environment that follows a specific file structure. Consequently, every command and script that you run rely on this file structure to ensure data reproducibility.
• Quick start tutorial: tutorial that you can follow to run a simple analysis with PAML. This type of analysis is suitable for running small tests with your dataset when using PAML programs as well as for timetree inference with small datasets.

These tutorials are based on a phylogenetics tool that I am working on at the moment, which I am still developing and is yet to be published. While some of the scripts/tools that you will find here have been validated and used in published research (Álvarez-Carretero et al., 2022), I am actively implementing new features as part of the current workflow of this pipeline as well as developing new scripts/tools. In other words, the code is not stable and I am still validating new features.

If you want to use the tools that I have developed as part of these tutorials/pipelines, please first contact me. Thank you :)