… of orthologous sequences among the taxa of interest. Most orthology inference programs
available for use in phylogenomics rely on small sets of pre-defined orthologs from model …

… of their homology relationships (orthology or paralogy). To … containing sequences, multiple
alignments and phylogenetic trees: … the search for orthologs or paralogs in these databases. …

… and also to trees based on the sequence similarity of individual orthologous proteins. We
found that our genomic trees based on the overall occurrence of orthologs did not agree well …

… A standard method of finding orthologs is to compare the sequence tree … sequences grouped
in 1000 families were created. The guidance trees contained 3093 orthologous sequence …

… similar sets of orthologs, especially at short evolutionary distances. Synteny also can aid in
… of orthologs. Often, tree-based, sequence similarity- and synteny-based approaches can be …

… gene sequence evolution model, by including sequence … sequence evolution model that,
given gene sequence data allows: (1) orthology analysis, reconciliation analysis, and gene tree …

… For each of the FOGs we made multiple sequence alignments and derived the phylogenetic
tree. The procedure matches that for the COGs as part of the previously described …

… Finally, we review typical applications of orthologous genes, groups, and reconciled trees …
with both the human and dog genes because it is orthologous to more than one sequence in …

… trees (percentage of ortholog-sequence-concatenated trees exhibiting the same topology as
the model tree) and each ortholog tree (percentage of ortholog trees … as the model tree) at …

… It uses a heuristics based upon Pearson’s correlation matrix of sequence distances to
decides upon speciation and duplication events without a species tree. Sets containing out-…