To evaluate the performance of TreeFix-DTL, we develop a thorough simulation framework that accounts for variations in species tree sizes, rates of gene evolution, alignment lengths, rates of duplication, transfer, and loss, (DTL) and species tree errors.
As genomes may undergo large-scale changes during evolution, global alignments using the Mauve alignment tool [ 17] were performed by pairwise comparison of the seven C. concisus strains with the reference BAA-1457 strain.
DSH conducted comparative genome analysis and evolution, sequence alignment, phylogenetic analysis and drafted the manuscript.
For evaluating the patterns of molecular evolution, codon alignment of the coding regions was created using MACSE, which allows the identification of frameshift events [ 87].
We identified a total of 86 WRKY genes from B. distachyon and explored their chromosomal distribution and evolution, domain alignment, promoter cis-elements, and expression profiles.
Rip sequences were aligned using the ProGraphMSA program, which implements the evolution-aware alignment [ 65, 66].
Our current work is focussed on inferring multi-rate models of codon evolution from alignments, and in particular the development of a Genetic Algorithm [18] for multi-rate codon model selection.
Since phylogeny-based methods of detecting positive selection do not take into consideration the effects of recombination on sequence evolution, gene alignments were analyzed using GARD (Genetic Algorithms for Recombination Detection) to estimate recombining breakage points [ 27, 28].
However, it is important to know how closely algorithmic alignments produced through optimization of any chosen target function reflect an evolution-based alignment of the appropriate amino acid sequences, e.g. the one, which juxtaposes the positions in the compared proteins originating from the same position in their common predecessor.
We note that no corresponding terms enter the slip rates, or the evolution of the alignment tensors, which are fully described by terms characterizing motion of already generated dislocations.
We used ModelGenerator (Keane et al. 2006) to choose an appropriate model of sequence evolution for the alignment.
