TREVoSim Command Line Suppressing Warnings In Analyses

This document addresses a user query regarding suppressing warnings in TREVoSim analyses when running the software from the command line. Specifically, the user is encountering "Warning, unresolvable clades" messages and seeks a command-line option to automatically acknowledge these warnings. This article provides a comprehensive exploration of this issue, offering potential solutions, workarounds, and a deeper understanding of how TREVoSim handles warnings during analyses.

Understanding the "Warning, Unresolvable Clades" Message

When working with TREVoSim, the "Warning, unresolvable clades" message indicates that the software has encountered difficulties in resolving the relationships between certain groups (clades) within your phylogenetic analysis. These warnings can arise from various factors, including:

• Data limitations: Insufficient data or conflicting signals in your input data can make it challenging for TREVoSim to construct a fully resolved phylogenetic tree. This is a common issue when dealing with incomplete datasets or when the evolutionary relationships between taxa are complex and difficult to discern.
• Model misspecification: The phylogenetic models used in TREVoSim are simplifications of real-world evolutionary processes. If the chosen model does not adequately capture the complexities of your data, it can lead to unresolved clades and associated warnings. For instance, using a simple model when the data exhibits complex patterns of rate variation or heterotachy can result in such warnings.
• Search limitations: Phylogenetic analyses often involve searching a vast space of possible tree topologies. If the search algorithm is not run for long enough or if it gets trapped in local optima, it may fail to find the optimal tree, leading to unresolved clades. This is particularly relevant for large datasets where the search space is enormous.
• Parameter settings: Certain parameter settings within TREVoSim can influence the resolution of clades. For example, the branch length prior or the tree prior can affect the posterior probability distribution of trees and, consequently, the resolution of the resulting phylogeny. Incorrect or inappropriate prior settings can sometimes lead to warnings about unresolvable clades.

It's crucial to understand the underlying reasons for these warnings in your specific analysis. Ignoring them can lead to inaccurate or misleading results. While automatically suppressing warnings might seem convenient, it's essential to investigate the cause and address it appropriately. This may involve refining your data, adjusting your model settings, or increasing the search effort.

Addressing the User's Query: Command-Line Option for Suppressing Warnings

As the user pointed out, a direct command-line option to automatically