Parsimony analysis of phylogenomic datasets (I): scripts and guidelines for using TNT (Tree Analysis using New...

Area of Science:

• Computational Biology
• Phylogenetics
• Bioinformatics

Background:

• Model-based phylogenetic analyses often rely on unrealistic assumptions and struggle with missing data.
• Parsimony methods provide a valuable alternative for phylogenomic analysis, especially with large datasets.
• Comparing parsimony and model-based trees can reveal topological differences and potential analysis artifacts.

Purpose of the Study:

• To introduce and detail the use of TNT (Tree Analysis using New Technology) software for phylogenomic analysis.
• To provide a suite of scripts tailored for efficient phylogenomic data handling and analysis within TNT.
• To demonstrate the application of TNT for phylogenetic reconstruction and support measure calculation.

Main Methods:

• Utilizing parsimony as an alternative to model-based phylogenetic methods.
• Employing TNT software for its computational efficiency and versatility in phylogenomic analyses.
• Developing and applying custom scripts for data concatenation, manipulation, and phylogenetic reconstruction.

Main Results:

• TNT enables rapid and computationally efficient phylogenomic analyses.
• Provided scripts facilitate diverse analyses including data formatting, occupancy variation, and support calculations.
• Demonstrated effective phylogenetic reconstruction using both concatenated and single-gene matrices.

Conclusions:

• TNT is a powerful and efficient tool for phylogenomic analysis, particularly when dealing with complex datasets and missing data.
• The provided scripts enhance the utility of TNT for specific phylogenomic workflows.
• Parsimony analysis in TNT facilitates in-depth investigation of phylogenetic tree topologies and potential artifacts.