Additional file 1:

Different ins/del rates between informational genes and non-informational genes. A, estimation was based on the select-genes trees; B, estimation was based on the common-genes trees. Only constant rates with no rate variation are shown, and the y = x line is also shown.

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Additional file 2:

Insertion/deletion rates of non-informative genes in different phylogenetic groups estimated with rate variation. Estimation was based on the select-genes trees. All the informational genes were excluded from the estimation.

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Additional file 3:

Insertion/deletion rates between informational genes and noninformational genes in COG classification. Estimation was based on the select-genes trees.

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Additional file 4:

Information on phylogeny construction using different methods.

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Additional file 5:

Boxplot of tree length of the select-genes tree and the common-genes tree from each group. Group names are shown in the first three letters (except MYB for Mycobacterium, MYP for Mycoplasma. For each group, tree length of the select-genes tree is on the left, and that of the common-genes tree is on the right.

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Additional file 6:

Alpha values based on different phylogenies. Estimation are based on possible alternative phylogenies for the common genes, which are sorted from best supported to lest supported.

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Additional file 7:

Alpha values based on different phylogenies. Estimation are based on possible alternative phylogenies for the selected genes, which are sorted from best supported to lest supported.

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Additional file 8:

The deletion of ribosomal proteins in Streptococcus mutans UA159 (GenBank accession: AE014133).

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Additional file 9:

Small α change after excluding informational genes compared with excluding the most conserved genes. A, Estimation was based on the select-genes trees; B, Estimation was based on the common-genes trees. Each bar represents a group and all groups were sorted according to their ratios. The ratios are obtained from Table 5.

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Additional file 10:

α value after informational genes were removed using different cutoffs on e-value and match length in identifying informative genes. Estimation was based on the select-genes trees. Maximum likelihood estimation was conducted by only using the best supported phylogeny of each group to reduce computational burden.

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Additional file 11:

Simulation methods and results.

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