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The calculations carried out here are of estimated character, and they should to be verified experimentally.
The BBM analysis was conducted with estimated character state frequencies (F81) and gamma-distributed rate variation between sites.
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Although our earlier approach [11] proved to be very effective in estimating character support and conflict, as well as supporting the case for the use of ESTs in phylogenetic analysis, it was clear more character information was needed to provide stronger support in the resolution of spermatophyte phylogeny.
As it remains unclear whether the MRCA of Oegopsida + Loliginidae lived earlier or later than the MCRA of Sepiolida + Loliginidae, we estimated the character state likelihoods for both ancestors.
It should also be stressed that the log- lk per character estimated from our initial character supermatrix (i.e. -21.07; see Table 5) is higher than those provided in [ 7] (i.e. -22.71; see Table 4, page 546 in [ 7]); this can be explained by the different number of characters but also by our use of the amino acid model mtREV+Γ8+I instead of just mtREV in [ 7].
AUC values in Figures 4 and 5 show that initial (non-trimmed) multiple sequence alignments lead to more incorrect confidence values than those estimated from characters selected by trimming methods.
The most pronounced difference is revealed while estimating the character of OIS signals' reflections from Es-layers.
The strategy we give here requires the proposer to estimate the character of the responder.
RidgeRace estimates ancestral character states on a phylogenetic tree.
This function estimates ancestral character states by maximum likelihood optimization [ 45].
Felsenstein [ 54] provided the details of the general procedure for estimating the character values in the ancestors.
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CEO of Professional Science Editing for Scientists @ prosciediting.com