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Table 3 Evaluation of SiLiX performances on mitochondrial genes of metazoan taxa.

From: Ultra-fast sequence clustering from similarity networks with SiLiX

Gene Nb. Seq. Nb. SiLiX families Nb. Seq. 1st fam. (%) Nb. Seq. 2nd fam. (%) Nb. Seq. 3rd fam. (%) Nb. Singletons (%)
ATP8 1815 26 959 (52.8) 294 (16.2) 144 (7.9) 258 (14.2)
ATP6 1821 2 1814 (99.6) 2 (0.1) - 5 (0.3)
COX1 1821 1 1820 (99.9) - - 1 (0.1)
COX2 1821 1 1818 (99.8) - - 3 (0.2)
COX3 1821 1 1821 (100) - - -
CYTB 1821 1 1820 (99.9) - - 1 (0.1)
ND1 1821 1 1821 (100) - - -
ND2 1821 11 1714 (94.1) 53 (2.9) 3 (0.2) 34 (1.9)
ND3 1821 2 1813 (99.6) 2 (0.1) - 6 (0.3)
ND4 1821 2 1812 (99.5) 2 (0.1) - 7 (0.4)
ND4L 1821 7 1758 (96.5) 4 (0.2) 3 (0.2) 47 (2.6)
ND5 1821 2 1815 (99.7) 2 (0.1) - 4 (0.2)
ND6 1821 16 1366 (75.0) 313 (17.2) 55 (3.0) 45 (2.5)
  1. Protein-coding genes were extracted from complete mitochondrial genomes of 1821 different metazoan species, and clustered using SiLiX (see text). For each of the 13 genes, we indicate the number of sequences present in the dataset, the number of families (containing at least 2 sequences) identified by SiLiX that contained these sequences, and the number and percentage of sequences included in the 3 largest SiLiX families (when they exist), as well as the number and percentage of singletons (SiLiX families containing one single sequence).