Table 2 Qualitative assessment of mtDNA haplogroup classification tools. Performance of each tool is evaluated across different features and represented on a color scale based on the level of performance: green triangle pointing up for good, orange square for fair, and red triangle pointing down for low performance.

From: A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data

  1. Haplogroup classification accuracy of each tool was categorized into three ranges based on the predicted probabilities by each application: tools with a predicted probability of incorrectly classifying a haplogroup below 1% were represented as good performance, for a fair performance was established a range between 1.01% and 10%, and as low performance tools with a predicted probability higher than 10.01%. For computation time, three intervals were established: tools that classified samples in less than a minute were defined as good performance, from 1 to 5 min were categorized as fair performance, and those tools that required more than an hour were represented as low performance. Regarding the PhyloTree database used, it was represented as low performance those tools which are not updated to the latest version of Phylotree, Build 17, and those that allow the latest version as high performance. Multi-sample function was evaluated based on the possibility of cohort analysis. Tools that allow to process these functions were defined as good performance, tools that allow processing several samples by using a loop through a command-line were categorized as fair performance, and tools without this ability were represented as low performance. Based on the file format supported two categories were established: tools that support various input format files categorized as high performance and those that only support one format file that are represented as low performance. The user interface was divided into two categories, tools based on web or desktop applications defined as good performance, and tools developed exclusively for CLI as low performance. The tool maintenance was classified into two classes, tools updated continually or have been recently released, both identified as good performance, and tools that have not been updated during the last years. The last feature is the presence or not of additional functions; tools that have other functions implemented are categorized as good performance. Those tools without more functions were determined as low performance.
Back to article page