TMRS: an algorithm for computing the time to the most recent substitution event from a multiple alignment column

Table 5 Correlation with other conservation measures

Significance measure	Spearman’s correlation with true \(t_{\text {MRS}}\)
\(t_{\text {MRS}}(q<0.01)\)	0.965
\(t_{\text {MRS}}(q<0.1)\)	0.938
\(t_{\text {MRS}}(q<1)\)	0.858
Reconstruction (\(q<1\))	0.905
Alignment (\(q<1\))	0.338
Entropy	0.301
Pairwise	0.344
Phastcons	0.112
Phylop	0.108
Gerp	0.129

We show Spearman’s correlation coefficient with the true \(t_{\text {MRS}}\) obtained from simulation and several measures for nucleotide conservation. The first three columns represent \(t_{\text {MRS}}\) computed by our exact algorithm with filtering by q values. ‘reconstruction’ represents approximate \(t_{\text {MRS}}\) values estimated from reconstruction of ancestral states. ‘alignment’ represents approximate \(t_{\text {MRS}}\) values estimated from closest extant species which has different nucleotide base from the nucleotide of the target species. ‘entropy’ represents the negative information entropy of the base frequency of alignment column. ‘pairwise’ represents the pairwise alignment similarity of alignment column. ‘phastcons’ represents the posterior probability of conservation at the alignment column. ’phylop’ represents the p-values of negative selection. ‘gerp’ represents the ‘rejected substitution’ values

ISSN: 1748-7188