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Genes are rearranged in the genome by evolutionary events such as inversion, transposition, and inverted transposition, collectively called genome rearrangements [1] [3].
While the RBBH method was proven to provide a solid bidirectional bridge between orthology and bidirectional best hits inferred from sequence similarity [ 19], it is by far not perfect given its limitations caused by evolutionary events such as gene loss and gene duplications or by incomplete genomic sequences.
Motivation: Gene family evolution is driven by evolutionary events such as speciation, gene duplication, horizontal gene transfer and gene loss, and inferring these events in the evolutionary history of a given gene family is a fundamental problem in comparative and evolutionary genomics with numerous important applications.
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Evolutionary events such as loss and acquisition of genes by lateral transfer events along each evolutionary branch results in lineage-specific genes, some of which may have been subsequently incorporated into the O2-responsive stimulon.
Evolutionary events such as speciation, gene duplication, and loss, accompanied by changes on the single nucleotide level, have generated an overwhelming amount of diversity in all domains of life.
Evolutionary events (such as rearrangements, selection pressure) are important factors which result in compositional variation along the sequence.
An essential component of such studies is the accurate inference of virus evolutionary rates as these enable the use of phylogenetic trees to date important evolutionary events such as host switches, geographical range expansions and changes in population sizes.
Evolutionary events, such as gains and losses of genes were shown to be influenced by their location on a chromosome [ 64].
Metabolic networks are believed to evolve via evolutionary events such as gene duplication [ 21- 23] and horizontal gene transfer [ 24].
Functional divergence of a protein family can occur after major evolutionary events such as gene duplication or speciation.
The biological network alignment may be much harder due to the complex evolutionary events such as gene mutations and duplications.
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