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...en released. HCOP currently collates orthology assertions from eggNOG (34), Ensembl Compara (2), HGNC, HomoloGene (31), InParanoid (35), OMA (36), OrthoDB (37), OrthoMCL (38), PANTHER (39), PhylomeDB =-=(40)-=-, Treefam (41) and ZFIN (18) into a single tool, enabling comparison of these data to identify a consensus orthology prediction for a specified human gene or set of genes. Data are integrated using pr...

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...r the descendant partitions have, at least one, common speciessor not (i.e. using a Species Overlap Score of 0). The resulting orthology and paralogy predictions can be accessedsthrough phylomeDB.org =-=(19)-=-. These predictions have been used in subsequent analyses such as orthology-basedsfunctional annotation, identification of gene expansions or duplication dating.sSpecies tree reconstruction. A phyloge...

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...utlier and is indicated by a black dot. A FLOCK OF GENOMESsevolution that subsequently increased on the avian stem lineage. Gene-based phylogeny and molecular evolution We used the PhylomeDB pipeline =-=(19)-=- to identify 337 single-copy orthologous gene sequences (17) from 22 tetrapod genomes (table S10). Phylogenetic analysis of a concatenated alignment of these genes (fig. S10) produced a tree congruent...

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...roteins of 11 other fully sequenced plant genomes (Supplemental Table 11), including S. tuberosum and S. lycopersicum (Figure 3). The resulting 35,182 phylogenetic trees, available through PhylomeDB (=-=Huerta-Cepas et al., 2014-=-), were scanned to predict phylogenybased orthology and paralogy relationships (Gabaldón, 2008), detect and date duplication events (Huerta-Cepas and Gabaldón, 2011), and transfer annotations to S. co...

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...utlier and is indicated by a black dot. A FLOCK OF GENOMESsevolution that subsequently increased on the avian stem lineage. Gene-based phylogeny and molecular evolution We used the PhylomeDB pipeline =-=(19)-=- to identify 337 single-copy orthologous gene sequences (17) from 22 tetrapod genomes (table S10). Phylogenetic analysis of a concatenated alignment of these genes (fig. S10) produced a tree congruent...

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...s were highly similarswhen each phylome was used independently. All gene trees, alignments and orthology andsparalogy calls for the five phylomes are available through phylomeDB (htp://phylomedb.org;s=-=(68)-=-).sPhylogeny based orthology predictionssThe species overlap algorithm described in (153) was used to detect speciation events in allsphylome trees as implemented in the ETE toolkit (154). A comprehen...

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...utlier and is indicated by a black dot. A FLOCK OF GENOMESsevolution that subsequently increased on the avian stem lineage. Gene-based phylogeny and molecular evolution We used the PhylomeDB pipeline =-=(19)-=- to identify 337 single-copy orthologous gene sequences (17) from 22 tetrapod genomes (table S10). Phylogenetic analysis of a concatenated alignment of these genes (fig. S10) produced a tree congruent...

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...utlier and is indicated by a black dot. A FLOCK OF GENOMESsevolution that subsequently increased on the avian stem lineage. Gene-based phylogeny and molecular evolution We used the PhylomeDB pipeline =-=(19)-=- to identify 337 single-copy orthologous gene sequences (17) from 22 tetrapod genomes (table S10). Phylogenetic analysis of a concatenated alignment of these genes (fig. S10) produced a tree congruent...

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... to the development of numerousmethods (reviewed in 5) and databases, notably including EggNOG (6), Ensembl Compara (7), Inparanoid (8), MBGD (9), OrthoDB (10), OrthoMCL (11), Panther (12), PhylomeDB =-=(13)-=-, Plaza (14) and OMA (15). The OMA (Orthologous MAtrix) project is a method and database for the inference of orthologs amongst complete proteomes (i.e. the protein sequences associated for every prot...