Table 1.
List of software assessed for human mtDNA haplogroup classification. All the tools assessed classify mtDNA sequences according to the PhyloTree nomenclature by using the latest version Build 17. Two of them, MitoTool and Phy-Mer, remain outdated in regards of the PhyloTree built when this study was conducted.
| Tool | User interface | Release year | Version | Latest release | Database version | Input options | Execution time$ (seconds) |
|---|---|---|---|---|---|---|---|
| James Lick'sa | Web | 2010 | 0.19a | 2013.04.08 | Phylotree 17 | FASTA | 20–27 |
| Haplogrepb | Web / CLI* | 2011 | 2.2.4 | 2016.07.08 | Phylotree 17 | VCF | FASTA | 0.1 | 1–3 |
| MitoToolc | App | 2011 | 1.1.2 | 2013.11.02 | Phylotree 16 | FASTA | 2–3 |
| Haplofindd | Web | 2013 | – | 2013.01.12 | Phylotree 17 | FASTA | 11–15 |
| EMMAe | Web | 2013 | 13 | 2019.11.28 | Phylotree 17 | FASTA | 10–38 |
| Phy-Merf | Web / CLI* | 2015 | 1.0.0 | 2016.01.14 | Phylotree 16 | BAM | FASTA | 8–298 | 51 -54 |
| MitoSuiteg | App | 2017 | 1.0.9 | 2017.06.06 | Phylotree 17 | BAM | 10–340 |
| MixEmth | CLI | 2017 | 0.1 | 2017.05.09 | Phylotree 17 | BAM | 79–5034 |
| Haplochecki | Web / CLI* | 2019 | 1.1.0 | 2019.11.17 | Phylotree 17 | BAM | VCF | 3–14 | 1 -2 |
| Haplotrackerj | Web | 2020 | – | 2020.04.23 | Phylotree 17 | FASTA | 30–32 |
| HaploGrouperk | CLI | 2020 | – | 2020.08.17 | Phylotree 17 | VCF | 0.1 |
*CLI Command-line interface. $A range is provided given the differences among samples in the size of the input files.
a: https://dna.jameslick.com/mthap/; b: https://haplogrep.i-med.ac.at16; c: http://mitotool.org24,45; d: https://haplofind.unibo.it46; e: https://empop.online28; f: https://github.com/MEEIBioinformaticsCenter/phy-mer27; g: https://mitosuite.com25; h: https://github.com/svohr/mixemt30; i: https://github.com/genepi/haplocheck31; j: https://haplotracker.cau.ac.kr26; k: https://gitlab.com/bio_anth_decode/haploGrouper47.