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Because of the promising results obtained by machine learning (ML) approaches in several fields, every day is more common, the utilization of ML to solve problems in bioinformatics. In genomics, a current issue is to detect and classify transposable elements (TEs) because of the tedious tasks involved in bioinformatics methods. Thus, ML was recently evaluated for TE datasets, demonstrating better results than bioinformatics applications. A crucial step for ML approaches is the selection of metrics that measure the realistic performance of algorithms. Each metric has specific characteristics and measures properties that may be different from the predicted results. Although the most commonly used way to compare measures is by using empirical analysis, a non-result-based methodology has been proposed, called measure invariance properties. These properties are calculated on the basis of whether a given measure changes its value under certain modifications in the confusion matrix, giving comparative parameters independent of the datasets. Measure invariance properties make metrics more or less informative, particularly on unbalanced, monomodal, or multimodal negative class datasets and for real or simulated datasets. Although several studies applied ML to detect and classify TEs, there are no works evaluating performance metrics in TE tasks. Here, we analyzed 26 different metrics utilized in binary, multiclass, and hierarchical classifications, through bibliographic sources, and their invariance properties. Then, we corroborated our findings utilizing freely available TE datasets and commonly used ML algorithms. Based on our analysis, the most suitable metrics for TE tasks must be stable, even using highly unbalanced datasets, multimodal negative class, and training datasets with errors or outliers. Based on these parameters, we conclude that the F1-score and the area under the precision-recall curve are the most informative metrics since they are calculated based on other metrics, providing insight into the development of an ML application.