Table 3

Evaluation of SiLiX performances on mitochondrial genes of metazoan taxa.

Gene

Nb. Seq.

Nb. SiLiXfamilies

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)


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).

Miele et al. BMC Bioinformatics 2011 12:116   doi:10.1186/1471-2105-12-116

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