NUDIMAX: An accessible data-wrangling pipeline and wrapper for partitioned phylogenetic workflows
This utility facilitates rapid creation of multi-gene datasets for small to medium-scale partitioned phylogenetic analysis projects (e.g., a classic multi-gene Sanger phylogenetics project). It also includes wrappers for several useful bioinformatic packages (BLAST, MAFFT, IQ-TREE, and MrBayes).
It is primarily written for researchers who:
- need to pull and organize multi-gene data from GenBank for partitioned phylogenetic analysis
- have limited (or no) coding experience
- do not have access to (or experience with) LINUX-based or command-line systems
It is primarily written for the the Google Colab environment, which includes a basic user interface. However, it is also portable to Jupyter notebooks or (for larger datasets) an HPC.