Characteristics of the applied test data sets including the results of the test for substitution saturation in loop and stem partitions.
Repeating reconstruction of cox1 without the third codon position did not yield any well supported nodes that contradicted well supported nodes in the reconstruction using all three codon positions, which confirms the reliability of the result from the applied test for substitution saturation.
The aim of the present study was to characterise correlations between this novel test set, called the Test for Substitution Patterns (TSP) and commonly used tests of knee function.
Data partitions were tested for substitution saturation using a non-parametric statistical test implemented by DAMBE 4.5.47 [56].
This alignment was also tested for substitution saturation, which indicated good phylogenetic signal.
Each gene was tested for substitution saturation using plots of transitions and transversions against F84 distance in DAMBE v4.5 [ 34].
Individual data partitions were tested for substitution saturation using a non-parametric statistical test based on an information entropy index [ 52] implemented in DAMBE 5.0.23 [ 53].
The data were tested for substitution saturation using plots of the numbers of transitions (Ts) and transversions (Tv) against the F81 genetic distance [ 126].
Alignments for the first approach were individually tested for substitution saturation [ 34] using DAMBE [ 35], which indicated little saturation for COX1 and 28S rDNA sequences (i.e. Iss. significantly lower than Iss.c), but higher levels of saturation for the 16S and 12S rDNAs (Iss. higher than Iss.c).
The first evaluation of the test set, called the Test for Substitution Patterns (TSP), showed that subjects with ACL injury display more frequent and/or more clearly present substitution patterns on their injured, and to a lesser extent also on their uninjured side, than do uninjured controls.
