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Finally, using plant-wide substitution of alternative materials as an example, it is shown how potential stepchange improvements in both life cycle environmental impact and process economics can be achieved.
In this manuscript we focused on organism-wide substitution patterns and our validation process convincingly showed that HIV models outperformed existing empirical models on a variety of individual gene alignments.
(H ) Substitution frequency in and outside CpG islands, relative to genome-wide substitution frequencies.
Selection of partition-wide substitution models was done in Treefinder, using AIC.
The concatenated genes were used to estimate the transcriptome-wide substitution rates in protein coding genes.
It has been suggested that the process of speciation may cause increases in genome-wide substitution rates [ 7].
This is particularly important for aligning the species like rodents which have high genome-wide substitution rates.
Thirdly, we identified a very low overall genome-wide substitution frequency (7 point mutations/genome) in AS-30CQ (Table 1, Table 2) relative to AS-sens.
The observation that substitution rates at these loci are positively correlated to species richness suggests that genome-wide substitution rates are associated with net diversification.
To avoid these possible biases, our results are based on genome-wide substitution histories reconstructed in a maximum likelihood framework using a context-dependent evolutionary model.
We computed genome-wide substitution patterns in the mouse lineage from multiple alignments and compared them with substitution patterns in the human lineage.
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