This means that for the third codon position, 16 GTR models (but each employing the same (single) set of base frequencies) will be estimated, one for each neighbouring base combination, resulting in 80 free evolutionary parameters to be estimated for the third codon position (compared to 5 free evolutionary parameters for the first codon position and the second codon position).
2 p-value – Multiple testing corrected p-values for the differences in the maximum likelihood estimates of the two models fit. 3 Sites – number of codons analyzed, 4 dn/ds – dn/ds for the model where one dn/ds ratio is estimated for the entire evolutionary tree.
Using a list of OTUs specified by the user, for each gene, SCaFoS will select the sequence that best represents a given OTU, ideally, the longest and slowest evolving orthologous sequence; evolutionary distance, as an approximation of the evolutionary rate, is estimated for each sequence.
Evolutionary models were estimated for all alignments using MEGA5 [ 43].
The best evolutionary model was estimated for each alignment using MEGA5 software [ 67].
Using the alignment data and its corresponding chronogram, molecular evolutionary rates were estimated for each gene at each alignment position.
Then, the correlations between EAs and evolutionary rates were estimated for each group to see if the negative correlation pattern was maintained even after the effects of EBs on the rates were controlled as evenly as possible.
Phlebovirus-specific evolutionary rates were estimated for the RdRp, GP, N and NS genes, from a heterochronous data set of RVFV isolates using the UCLD relaxed molecular clock model implemented in BEAST.
These results also show that these parameters can be estimated accurately only for very recent evolutionary time-scales.
For these families, only one alternative model (model 1) was tested, for which two different evolutionary rates were estimated, one for the parental (w0) and another for the duplicated gene (w1).
