Table 1.
Performance of GenDecoder and the importance of using an appropriate taxonomic sampling
| Number of species | 54-Taxa multiple alignments | All-metazoans multiple alignments | |||
|---|---|---|---|---|---|
| #Concordant/total | FP/TP (%) | Number of concordant/total | FP/TP (%) | ||
| Annelida | 4 | 244/247 | 1.2 | 244/248 | 1.6 |
| Arthropoda | 87 | 5116/5222 | 2.1 | 5048/5265 | 4.3 |
| Brachiopoda | 2 | 122/123 | 0.8 | 118/124 | 5.1 |
| Cephalochordata | 5 | 303/303 | 0.0 | 305/306 | 0.3 |
| Cnidaria | 4 | 246/248 | 0.8 | 242/248 | 2.5 |
| Echinodermata | 11 | 671/676 | 0.7 | 672/678 | 0.9 |
| Hemichordata | 1 | 60/60 | 0.0 | 60/60 | 0.0 |
| Mollusca | 15 | 911/924 | 1.4 | 895/926 | 3.5 |
| Nematoda | 12 | 634/690 | 8.8 | 600/703 | 17.2 |
| Platyhelmynthes | 10 | 525/598 | 13.9 | 475/601 | 26.5 |
| Porifera | 3 | 176/178 | 1.1 | 176/178 | 1.1 |
| Vertebrata | 461 | 27 288/27 375 | 0.3 | 27 547/27 498 | 0.2 |
Note: discrepancies in the number of assignments between the two experiments are related with the different behaviour that the conservancy threshold manifests with different alignments (e.g. there were 598 and 601 assignments for platyhelminths in the two experiments).
#Concordant/total, number of assignments concordant with GenBank/total number of assignments. Unassigned codons, i.e. codons that either are not used or do not appear at conserved positions (in this case entropy > 2.0; gaps > 20%), are not considered in this table.
#FP/TP, false-positive rate. Non-concordant/concordant assignments × 100.