Table 2 Maximum classification accuracy scores when using Euclidean vs. Pearson’s correlation coefficient (PCC) as a distance measure
Maximum accuracy | ||||||||
|---|---|---|---|---|---|---|---|---|
Euclidean | PCC | |||||||
Data Set | No. of Seq. | Max Length (bp) | Min Length (bp) | Median Length (bp) | Norm. to Max Length (a) | Norm. to Median Length (b) | Norm. to Max Length (c) | Norm. to Median Length (d) |
Primates (Haplorrhini: 115, Strepsirrhini: 33) | 148 | 17531 | 15467 | 16554 | 98.6% | 100% | 100% | 100% |
Protists (Alveolata: 34, Rhodophyta: 46, Stramenopiles: 79) | 159 | 77356 | 5882 | 35660 | 89.3% | 90.6% | 96.2% | 91.2% |
Fungi (Basidiomycota: 30, Pezizomycotina: 104, Saccharomycotina:92) | 226 | 235849 | 1364 | 39154 | 70.1% | 82.6% | 87.9% | 89.3% |
Plants (Chlorophyta: 44, Streptophyta: 130) | 174 | 1999595 | 12998 | 128211 | 95.4% | 94.8% | 90.2% | 91.4% |
Amphibians (Anura: 161, Caudata:95, Gymnophiona: 34) | 290 | 28757 | 15757 | 17271 | 95.2% | 97.6% | 98.3% | 99.0% |
Mammals (Xenarthrans: 30, Bats: 54, Carnivores: 135, Even-toed Ungulates: 242, Insectivores: 40, Marsupials: 34, Primates: 148, Rodents and Rabbits: 147) | 830 | 17734 | 15289 | 16537 | 95.2% | 96.1% | 97.8% | 97.1% |
Insects (Coleoptera: 95, Dictyptera: 77, Diptera: 149, Hemiptera: 126, Hymenoptera: 47, Lepidoptera:294, Orthoptera: 110) | 898 | 20731 | 10662 | 15529 | 87.9% | 90.0% | 91.3% | 94.2% |
3 classes (Amphibians: 290, Mammals: 874, Insects: 1006) | 2170 | 28757 | 8118 | 16361 | 99.9% | 99.7% | 99.8% | 99.7% |
Vertebrates (Amphibians: 290, Birds: 553, Fish: 2313, Mammals: 874, Reptiles: 292) | 4322 | 28757 | 14935 | 16616 | 99.6% | 99.8% | 99.6% | 99.7% |
Table Average Accuracy | —— | —— | —— | —— | 92.4% | 94.6% | 95.7% | 95.7% |