Sequences that have not experienced substantial substitution saturation will show a linear relationship for both transitions and transversions versus sequence divergence; also, transitions will occur more often than transversions (Xia and Xie 2001).
Saturation plots revealed substantial substitution saturation in the third codon positions of 13 PCGs and rrnS (Additional file 13).
In contrast, the concatenated 4D-sites of 13 mitochondrial genes showed substantial substitution saturation (two tailed P value >0.05) and were excluded for further analysis.
This latter acid cannot be esterified by the standard Fischer Speier method, and its methyl ester undergoes substantial substitution of the nitro group when basic hydrolysis is attempted.
Substantial substitution of DNA G by 6-TG is well tolerated by cells and DNA 6-TG is not significantly miscoding during replication.
Sequence divergence is expected to be neither too conservative nor too diverged as to experience substantial substitution saturation; this saturation decreases phylogenetic information [ 57].
It revealed that the 18S and H3 sequences were unaffected by multiple hits (Iss < Iss.c; p < 0.05), but suggested the presence of substantial substitution saturation in the 16S sequence (Iss > Iss.c; p < 0.05).
The evolutionary divergence between the various duplicate pairs, both LSDs and population duplicates, suggests that at least some of the duplication events are relatively old, allowing time for accumulation of substantial substitution.
If prices rose over a longer time horizon absent the sharp reversals in prices the world oil market saw in the 1990s, and as one would design a policy aimed at cutting long-term consumption then more substantial substitutions would occur.
Our analysis revealed a substantial elevation in substitution rate for rrn5 in S. latifolia.
Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees.
