# DIOPT Documentation ## expand\_more #### Added 2025: DIOPT Version 10 documentation pages See this page: [https://www.flyrnai.org/DIOPT\_documentation\_v10.html](https://www.flyrnai.org/DIOPT_documentation_v10.html) #### DIOPT Version 9 documentation Website: [https://www.flyrnai.org/cgi-bin/DRSC\_orthologs.pl](https://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl) - [Version 8 information](/diopt-version-8) ### About DIOPT The identification of orthologs is commonly used for bioinformatics activities such as data mining and establishing models for human diseases. Moreover, our group notes that researchers analyzing the results of screens performed at the Drosophila RNAi Screening Center (DRSC) frequently wish to identify mammalian orthologs of the fly genes that were "hits" (positive results) in their screens. In helping DRSC screeners to identify orthologs using existing tools and algorithms, we recognized a need for a user-friendly approach to viewing and comparing ortholog predictions obtained using different tools and algorithms. This was our motivation in developing DIOPT. To facilitate identification of orthologs specifically of human disease-associated genes, we further developed DIOPT-DIST. Information about our approaches to development of both tools is summarized below. ### The DIOPT Approach Many tools have emerged to meet the need to identify orthologs. However, low coverage and heterogeneity of these tools present an obstacle to scientists who want to identify a one or a few highest-confidence orthologs for a given gene of interest or conversely, want to cast a wide net and follow up on all possible orthologs of a gene. Our goal is to provide an easy-to-use resource that facilitates summary, comparison and access to various sources of ortholog predictions. DIOPT integrates human, mouse, fly, worm, zebrafish and yeast ortholog predictions made by Ensembl Compara, HomoloGene, Inparanoid, Isobase, OMA, orthoMCL, Phylome, RoundUp, and TreeFam. DIOPT lets users find ortholog pairs for a specified gene or genes identified by one, many or all of these published approaches. This provides a streamlined method for integration, comparison and access to orthology predictions originating from algorithms based on sequence homology, phylogenetic trees, and functional similarity. DIOPT calculates a simple score indicating the number of tools that support a given orthologous gene-pair relationship, as well as a weighted score based on functional assessment using high quality GO molecular function annotation of all fly-human orthologous pairs predicted by each tool. Differences in the algorithms used by each tool to predict orthologous relationship is one source of difference in the set of predictions made by one tool versus another. However, we also note that some of these differences might be attributable to use of different genome annotation releases used by some tools versus others, and that not all tools cover all of the species that we include in the DIOPT tool (see Tables 1,2 and 3). DIOPT also displays protein and domain alignments, including percent amino acid identity, for predicted ortholog pairs. These should help you to identify the most appropriate matches among multiple possible orthologs. The following summary figures and tables help to explain our approach and summarize the tools and algorithms included in DIOPT. Sort ## Summary Information and Publications for the Tools Integrated in Table 1: Summary Information and Publications for the Tools Integrated in DIOPT Sort **Prediction Method** **Source** **Prediction Algorithm** **Coverage** **PMID** [Compara](http://ensembl.org/info/docs/api/compara/index.html) Ensembl Phylogenetic approach 228 species (vs 104) [19029536](http://www.ncbi.nlm.nih.gov/pubmed/19029536) [Homologene](http://www.ncbi.nlm.nih.gov/homologene) NCBI Combination of BBH\*, tree and synteny 21 species (vs. 68) [11125071](http://www.ncbi.nlm.nih.gov/pubmed/11125071) [Inparanoid ](http://inparanoid.sbc.su.se/cgi-bin/index.cgi) Stockholm University, Sweden BBH\* approach to identify orthologs and in-paralogs 273 species (vs. 8) [11743721](http://www.ncbi.nlm.nih.gov/pubmed/11743721) [25429972](http://www.ncbi.nlm.nih.gov/pubmed/25429972) [Isobase](http://groups.csail.mit.edu/cb/mna/isobase/) MIT Sequence and PPI\* network alignments 5 species (vs.2, Nov. 2014) [21177658](http://www.ncbi.nlm.nih.gov/pubmed/21177658) [OMA](http://omabrowser.org/cgi-bin/gateway.pl) CBRG, ETH Zurich BBH\*, global sequence alignments QFO2020 [17545180](http://www.ncbi.nlm.nih.gov/pubmed/17545180) [OrthoDB](http://cegg.unige.ch/orthodb6) University of Geneva Phylogenetic approach >7302 species (vs.10.1) [20972218](http://www.ncbi.nlm.nih.gov/pubmed/20972218) [25428351](http://www.ncbi.nlm.nih.gov/pubmed/25428351) [orthoMCL](http://www.orthomcl.org/cgi-bin/OrthoMclWeb.cgi) University of Pennsylvania Markov Cluster algorithm 605 species (vs. 6.6) [12952885](http://www.ncbi.nlm.nih.gov/pubmed/12952885) [Phylome](http://phylomedb.org/) Centre for Genomic Regulation (CRG), Spain Reconstruction of evolutionary histories of all genes in a genome, also known as phylome. 1059 species,120 Phylomes (vs. 4) QFO2014 [17962297](http://www.ncbi.nlm.nih.gov/pubmed/17962297) [24275491](http://www.ncbi.nlm.nih.gov/pubmed/24275491) [RoundUp](http://www.ncbi.nlm.nih.gov/pubmed/22247275) Harvard Medical School RSD\*, modified BBH\* 2044 species (Apr 2013) [16777906](http://www.ncbi.nlm.nih.gov/pubmed/16777906) [TreeFam](http://www.treefam.org/) Wellcome Trust Sanger Institute Manually curated based on trees 109 species (vs. 9) [16381935](http://www.ncbi.nlm.nih.gov/pubmed/16381935) [24194607](http://www.ncbi.nlm.nih.gov/pubmed/24194607) [Panther ](http://pantherdb.org/) University of Southern California Phylogenetic approach 132 species (vs. 16.1) [26578592 ](http://www.ncbi.nlm.nih.gov/pubmed/26578592) [HGNC ](http://www.genenames.org/) European Bioinformatics Institute (EMBL-EBI) Manually curated 3 species (Aug 2021) [ZFIN ](http://zfin.org/ZFIN) Zebrafish Model Organism Database Sequence similarity analysis and manual curation 4 species (July 2021) [Domainoid ](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3137-2) Stockholm University,Sweden Infer orthology on the domain level QFO2020 [31660857 ](http:/www.ncbi.nlm.nih.gov/pubmed/31660857) [eggNOG](http://eggnogdb.embl.de) Embl, Germany Graph-based algorithms 5090 species (vs. 5.0) [26582926 ](http:/www.ncbi.nlm.nih.gov/pubmed/26582926) [OrthoFinder](http://www.stevekellylab.com/software/orthofinder) University of Oxford Graph-based algorithms Run code with 12 ref proteome (2020) [26578592](http:/www.ncbi.nlm.nih.gov/pubmed/26578592) [OrthoInspector](http://lbgi.igbmc.fr/orthoinspector/OrthoInspector) Institut de Génétique et de Biologie Moléculaire et Cellulaire A novel orthogroup inference algorithm that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy. QFO 2020 [21219603](http:/www.ncbi.nlm.nih.gov/pubmed/21219603) [Hieranoid](http://hieranoid.sbc.su.se) Stockholm Bioinformatics Center The OrthoInspector algorithm is divided into three main steps. First, the results of a Blast all-versus-all (proteomes are blasted against each other) is provided by the user and is parsed to find all the Blast best hits for each protein and to create the groups of inparalogs. Second, the inparalog groups for each organism are compared in a pairwise fashion to define potential orthologs and/or in-paralogs. Third, best hits that contradict the potential orthology between entities are detected. QFO 2020 [27742821](http:/www.ncbi.nlm.nih.gov/pubmed/27742821) [ECGA](https://ecocyc.org/) ECOCYC Genome Database Collection Manually curated 2 species (Feb 2021) NA [SGD](https://www.yeastgenome.org/) Saccharomyces Genome Database Manually curated 1 species of paralogs (Oct 2020) NA [sonicParanoid](http://iwasakilab.k.u-tokyo.ac.jp/sonicparanoid/) University of Tokyo Graph-based algorithms Run code with 12 ref proteome (2020) [30032301](http:/www.ncbi.nlm.nih.gov/pubmed/30032301) [NCBI](https://www.ncbi.nlm.nih.gov/kis/info/how-are-orthologs-calculated/) NIH Details are not published. Combination of BBH, tree and synteny. Human2Vertebrate [SwiftOrtho](https://github.com/Rinoahu/SwiftOrtho) Iowa State University Iowa State University NA [31648300](http:/www.ncbi.nlm.nih.gov/pubmed/31648300) BBH, Best Blast Hits RSD, Reciprocal Smallest Distance PPI, Protein-Protein Interactions ## Genome Release Information Table 2A: Genome Release Information for the Tools Integrated in DIOPT (Version 9) Sort **Worm** **Fish** **Fly** **Human** **Mouse** **Yeast** **Fission Yeast** **Frog** **Rat** **Thale cress** **Mosquito** **E coli** **Compara** WBcel235 GRCz11 BDGP6.32 GRCh38 GRCm39 R64-1-1 NA Xenopus_tropicalis_v9.1 Rnor_6.0 NA NA NA **Domainoid** ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 **ECGA** NA NA NA ECGA Feb 2021 NA NA NA NA NA NA NA ECGA Feb 2021 **eggNOG** WormBase Ensembl FlyBase Ensembl Ensembl SGD PomBase Ensembl Ensembl Araport VectorBase Ecocyc **HGNC** NA NA NA HGNC Aug 2021 HGNC Aug 2021 NA NA NA HGNC Aug 2021 NA NA NA **Hieranoid** ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 **Homologene** WS195 Zv9 FlyBase r5.48 GRCh38 GRCm38.p2 R64-1-1 ASM294v2 Xtropicalis_v7 Rnor_5.0 TAIR10 AgamP3.3 NA **Inparanoid** ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 **Isobase** Ensembl v59 NA Ensembl v59 Ensembl v59 Ensembl v59 Ensembl v59 NA NA NA NA NA NA **OMA** ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 **orthoDB** Refseq Refseq FlyBase Refseq Refseq NA NA Refseq Refseq Refseq VectorBase NA **OrthoFinder** ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 **OrthoInspector** ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 **orthoMCL** ref proteome 2020 ref proteome 2020 ref proteome 2020 HostDB HostDB FungiDB FungiDB ref proteome 2020 ref proteome 2020 ref proteome 2020 VectorBase ref proteome 2020 **Panther** ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 **Phylome** ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 **RoundUp** UniProt Apr 2013 UniProt Apr 2013 UniProt Apr 2013 UniProt Apr 2013 UniProt Apr 2013 UniProt Apr 2013 UniProt Apr 2013 UniProt Apr 2013 NA NA NA NA **SGD** NA NA NA NA NA SGD Oct 2020 NA NA NA NA NA NA **sonicParanoid** ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 **TreeFam** Ensembl v69 Ensembl v69 Ensembl v69 Ensembl v69 Ensembl v69 Ensembl v69 Ensembl v69 Ensembl v69 Ensembl v69 NA VectorBase NA **ZFIN** NA ZFIN Aug 2021 ZFIN Aug 2021 ZFIN Aug 2021 ZFIN Aug 2021 NA NA NA NA NA NA NA **NCBI** NA EntrezGene Oct 2021 NA EntrezGene Oct 2021 EntrezGene Oct 2021 NA NA EntrezGene Oct 2021 EntrezGene Oct 2021 NA NA NA **SwiftOrtho** ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 #### Table 2B: Additional Information About Genome Releases (Version 9) Sort Other Resource Version WormBase release280 FlyBase release6.40 RefSeq release207 (July 2021) EntrezGene 26-July-2021 ## Table 3. Maximum DIOPT score for each orthologous relationship ### **(version 9)** Sort **Orthologous Relationship** **Max score** **Type** **Relevant Tools** **bacteria-baker's yeast** 12 ortholog eggNOG; Panther; orthoMCL; Hieranoid; OMA; Phylome; sonicParanoid; Inparanoid; OrthoFinder; SwiftOrtho; OrthoInspector; Domainoid; **bacteria-fish** 12 ortholog Panther; SwiftOrtho; Phylome; Domainoid; sonicParanoid; orthoMCL; Hieranoid; OMA; OrthoFinder; eggNOG; OrthoInspector; Inparanoid; **bacteria-fission yeast** 12 ortholog OrthoInspector; Domainoid; OMA; OrthoFinder; Inparanoid; Hieranoid; SwiftOrtho; eggNOG; orthoMCL; Panther; sonicParanoid; Phylome; **bacteria-fly** 12 ortholog OMA; sonicParanoid; OrthoInspector; Domainoid; OrthoFinder; Inparanoid; orthoMCL; SwiftOrtho; eggNOG; Hieranoid; Panther; Phylome; **bacteria-frog** 11 ortholog SwiftOrtho; sonicParanoid; OrthoFinder; Domainoid; OrthoInspector; Hieranoid; Panther; Phylome; OMA; eggNOG; Inparanoid; **bacteria-human** 13 ortholog orthoMCL; Panther; OrthoFinder; Phylome; Domainoid; Inparanoid; SwiftOrtho; ECGA; OrthoInspector; eggNOG; Hieranoid; sonicParanoid; OMA; **bacteria-mosquito** 11 ortholog OrthoInspector; Inparanoid; SwiftOrtho; Panther; Domainoid; Phylome; OMA; OrthoFinder; Hieranoid; eggNOG; sonicParanoid; **bacteria-mouse** 12 ortholog Domainoid; eggNOG; OMA; sonicParanoid; Hieranoid; Panther; Phylome; Inparanoid; SwiftOrtho; orthoMCL; OrthoFinder; OrthoInspector; **bacteria-rat** 12 ortholog Hieranoid; OrthoInspector; OMA; orthoMCL; Inparanoid; SwiftOrtho; Domainoid; Panther; sonicParanoid; Phylome; eggNOG; OrthoFinder; **bacteria-thale cress** 12 ortholog OrthoInspector; Hieranoid; Inparanoid; sonicParanoid; Panther; SwiftOrtho; Phylome; eggNOG; OMA; Domainoid; OrthoFinder; orthoMCL; **bacteria-worm** 12 ortholog OrthoFinder; Panther; Phylome; OrthoInspector; orthoMCL; sonicParanoid; Inparanoid; Domainoid; SwiftOrtho; OMA; eggNOG; Hieranoid; **baker's yeast-fish** 16 ortholog SwiftOrtho; sonicParanoid; orthoMCL; OMA; Domainoid; Panther; Hieranoid; Phylome; RoundUp; OrthoFinder; TreeFam; eggNOG; OrthoInspector; Homologene; Compara; Inparanoid; **baker's yeast-fission yeast** 14 ortholog OMA; OrthoInspector; Homologene; Domainoid; Panther; Inparanoid; Phylome; OrthoFinder; orthoMCL; RoundUp; sonicParanoid; TreeFam; eggNOG; Hieranoid; **baker's yeast-fly** 16 ortholog OrthoInspector; Isobase; orthoMCL; Homologene; Panther; Phylome; Inparanoid; RoundUp; OrthoFinder; Domainoid; TreeFam; OMA; Compara; eggNOG; sonicParanoid; Hieranoid; **baker's yeast-frog** 15 ortholog SwiftOrtho; OrthoFinder; Panther; Phylome; RoundUp; TreeFam; OrthoInspector; Domainoid; Compara; OMA; sonicParanoid; Homologene; Hieranoid; Inparanoid; eggNOG; **baker's yeast-human** 17 ortholog Compara; OrthoFinder; Homologene; sonicParanoid; Inparanoid; OMA; SwiftOrtho; Isobase; OrthoInspector; Domainoid; Panther; Phylome; eggNOG; RoundUp; orthoMCL; TreeFam; Hieranoid; **baker's yeast-mosquito** 12 ortholog Phylome; Homologene; TreeFam; OrthoInspector; Inparanoid; OMA; Domainoid; sonicParanoid; OrthoFinder; eggNOG; Hieranoid; Panther; **baker's yeast-mouse** 17 ortholog Domainoid; orthoMCL; Isobase; OrthoFinder; Panther; OrthoInspector; Phylome; sonicParanoid; OMA; RoundUp; Hieranoid; TreeFam; Compara; eggNOG; Homologene; Inparanoid; SwiftOrtho; **baker's yeast-rat** 15 ortholog Hieranoid; OrthoFinder; OMA; eggNOG; Homologene; Panther; Inparanoid; OrthoInspector; orthoMCL; Domainoid; Phylome; SwiftOrtho; TreeFam; sonicParanoid; Compara; **baker's yeast-thale cress** 14 ortholog Panther; OrthoFinder; sonicParanoid; Domainoid; Phylome; TreeFam; OrthoInspector; Homologene; OMA; Inparanoid; Hieranoid; SwiftOrtho; eggNOG; orthoMCL; **baker's yeast-worm** 17 ortholog Compara; eggNOG; Hieranoid; OrthoFinder; sonicParanoid; orthoMCL; OrthoInspector; Homologene; Isobase; OMA; Inparanoid; SwiftOrtho; Panther; Phylome; Domainoid; RoundUp; TreeFam; **fish-fission yeast** 15 ortholog sonicParanoid; Panther; Phylome; RoundUp; OrthoFinder; TreeFam; OMA; orthoMCL; Homologene; Domainoid; Inparanoid; SwiftOrtho; eggNOG; Hieranoid; OrthoInspector; **fish-fly** 18 ortholog ZFIN; Hieranoid; Panther; OMA; Phylome; sonicParanoid; RoundUp; orthoMCL; TreeFam; OrthoFinder; Compara; Homologene; Inparanoid; SwiftOrtho; Domainoid; eggNOG; OrthoInspector; OrthoDB; **fish-frog** 16 ortholog OrthoFinder; OMA; Phylome; SwiftOrtho; RoundUp; sonicParanoid; TreeFam; Compara; OrthoInspector; Domainoid; OrthoDB; Homologene; eggNOG; Panther; Hieranoid; Inparanoid; **fish-human** 19 ortholog Hieranoid; NCBI; ZFIN; OrthoDB; OrthoInspector; Panther; Phylome; Homologene; RoundUp; TreeFam; Inparanoid; Compara; SwiftOrtho; Domainoid; orthoMCL; eggNOG; sonicParanoid; OMA; OrthoFinder; **fish-mosquito** 14 ortholog sonicParanoid; Homologene; Inparanoid; SwiftOrtho; OrthoDB; OrthoFinder; Panther; Phylome; Domainoid; TreeFam; OMA; eggNOG; OrthoInspector; Hieranoid; **fish-mouse** 18 ortholog sonicParanoid; ZFIN; Panther; Domainoid; Phylome; orthoMCL; RoundUp; TreeFam; eggNOG; OrthoInspector; Compara; Homologene; Hieranoid; Inparanoid; SwiftOrtho; OMA; OrthoFinder; OrthoDB; **fish-rat** 16 ortholog Hieranoid; eggNOG; Homologene; OrthoDB; Inparanoid; SwiftOrtho; Panther; sonicParanoid; Phylome; TreeFam; OrthoInspector; orthoMCL; Domainoid; Compara; OrthoFinder; OMA; **fish-thale cress** 15 ortholog Domainoid; Homologene; Inparanoid; sonicParanoid; OrthoDB; Hieranoid; SwiftOrtho; eggNOG; orthoMCL; Panther; OMA; OrthoFinder; Phylome; TreeFam; OrthoInspector; **fish-worm** 17 ortholog OMA; orthoMCL; OrthoDB; OrthoInspector; Hieranoid; Panther; Phylome; RoundUp; TreeFam; Homologene; Compara; sonicParanoid; Inparanoid; SwiftOrtho; OrthoFinder; Domainoid; eggNOG; **fission yeast-fly** 14 ortholog Domainoid; sonicParanoid; Homologene; Hieranoid; Inparanoid; OMA; eggNOG; Panther; Phylome; RoundUp; TreeFam; orthoMCL; OrthoInspector; OrthoFinder; **fission yeast-frog** 14 ortholog OrthoInspector; OMA; Hieranoid; Panther; Phylome; RoundUp; TreeFam; OrthoFinder; Homologene; Inparanoid; eggNOG; SwiftOrtho; sonicParanoid; Domainoid; **fission yeast-human** 15 ortholog Domainoid; OMA; Homologene; orthoMCL; Inparanoid; OrthoInspector; Hieranoid; SwiftOrtho; OrthoFinder; eggNOG; sonicParanoid; Panther; Phylome; RoundUp; TreeFam; **fission yeast-mosquito** 12 ortholog Panther; OMA; OrthoFinder; Phylome; TreeFam; Hieranoid; eggNOG; OrthoInspector; sonicParanoid; Homologene; Inparanoid; Domainoid; **fission yeast-mouse** 15 ortholog Inparanoid; SwiftOrtho; Hieranoid; orthoMCL; Panther; Phylome; eggNOG; RoundUp; TreeFam; OMA; OrthoInspector; Domainoid; OrthoFinder; Homologene; sonicParanoid; **fission yeast-rat** 14 ortholog Panther; SwiftOrtho; orthoMCL; Phylome; OrthoInspector; TreeFam; sonicParanoid; Domainoid; eggNOG; Hieranoid; Homologene; OrthoFinder; OMA; Inparanoid; **fission yeast-thale cress** 14 ortholog Homologene; Panther; orthoMCL; Inparanoid; Phylome; SwiftOrtho; sonicParanoid; TreeFam; OrthoFinder; eggNOG; Domainoid; Hieranoid; OrthoInspector; OMA; **fission yeast-worm** 15 ortholog OrthoInspector; Domainoid; OMA; Homologene; Inparanoid; sonicParanoid; SwiftOrtho; OrthoFinder; Hieranoid; orthoMCL; eggNOG; Panther; Phylome; RoundUp; TreeFam; **fly-frog** 16 ortholog OMA; OrthoDB; Hieranoid; Panther; Phylome; RoundUp; OrthoFinder; TreeFam; Compara; sonicParanoid; eggNOG; Homologene; OrthoInspector; Inparanoid; Domainoid; SwiftOrtho; **fly-human** 19 ortholog Domainoid; Hieranoid; Homologene; OrthoFinder; orthoMCL; sonicParanoid; Inparanoid; OrthoDB; SwiftOrtho; Isobase; eggNOG; Panther; Phylome; RoundUp; TreeFam; OrthoInspector; User_Submission; Compara; OMA; **fly-mosquito** 13 ortholog Homologene; TreeFam; Inparanoid; Hieranoid; OrthoInspector; eggNOG; sonicParanoid; OrthoDB; OMA; Panther; OrthoFinder; Phylome; Domainoid; **fly-mouse** 18 ortholog Domainoid; Compara; OrthoInspector; OrthoFinder; Hieranoid; orthoMCL; sonicParanoid; eggNOG; OrthoDB; Isobase; Homologene; Panther; Phylome; Inparanoid; OMA; RoundUp; TreeFam; SwiftOrtho; **fly-rat** 16 ortholog Hieranoid; OrthoDB; orthoMCL; sonicParanoid; OMA; Panther; Phylome; OrthoFinder; TreeFam; eggNOG; Compara; OrthoInspector; Homologene; Domainoid; Inparanoid; SwiftOrtho; **fly-thale cress** 15 ortholog Panther; sonicParanoid; Phylome; OrthoFinder; TreeFam; Homologene; Inparanoid; orthoMCL; SwiftOrtho; eggNOG; OrthoInspector; Domainoid; OMA; Hieranoid; OrthoDB; **fly-worm** 18 ortholog OMA; Domainoid; sonicParanoid; OrthoFinder; Homologene; OrthoDB; Hieranoid; Isobase; Inparanoid; Panther; SwiftOrtho; OrthoInspector; Phylome; RoundUp; eggNOG; TreeFam; orthoMCL; Compara; **frog-human** 17 ortholog Compara; NCBI; eggNOG; Domainoid; Homologene; Inparanoid; OrthoDB; Hieranoid; SwiftOrtho; OrthoFinder; Panther; OMA; sonicParanoid; Phylome; OrthoInspector; RoundUp; TreeFam; **frog-mosquito** 14 ortholog Panther; sonicParanoid; Phylome; TreeFam; Homologene; OrthoFinder; Inparanoid; Domainoid; eggNOG; OrthoInspector; SwiftOrtho; Hieranoid; OMA; OrthoDB; **frog-mouse** 16 ortholog OrthoInspector; Homologene; Domainoid; Inparanoid; SwiftOrtho; Hieranoid; OrthoDB; sonicParanoid; OrthoFinder; Panther; eggNOG; Phylome; RoundUp; TreeFam; OMA; Compara; **frog-rat** 15 ortholog OMA; Homologene; sonicParanoid; Panther; Inparanoid; Hieranoid; Phylome; SwiftOrtho; TreeFam; OrthoInspector; Compara; eggNOG; OrthoFinder; Domainoid; OrthoDB; **frog-thale cress** 14 ortholog Panther; eggNOG; Hieranoid; Phylome; TreeFam; Homologene; OrthoInspector; sonicParanoid; Inparanoid; OrthoFinder; SwiftOrtho; OMA; Domainoid; OrthoDB; **frog-worm** 16 ortholog Compara; eggNOG; Domainoid; OrthoDB; Homologene; sonicParanoid; OrthoInspector; OrthoFinder; Inparanoid; Panther; SwiftOrtho; Phylome; OMA; Hieranoid; RoundUp; TreeFam; **human-mosquito** 14 ortholog Phylome; TreeFam; Homologene; eggNOG; OMA; Inparanoid; Domainoid; SwiftOrtho; OrthoFinder; OrthoInspector; Hieranoid; OrthoDB; Panther; sonicParanoid; **human-mouse** 20 ortholog OrthoInspector; OrthoDB; Domainoid; Isobase; OrthoFinder; Panther; Homologene; Phylome; HGNC; RoundUp; Inparanoid; NCBI; TreeFam; Hieranoid; SwiftOrtho; eggNOG; Compara; sonicParanoid; OMA; orthoMCL; **human-rat** 18 ortholog OMA; Compara; Hieranoid; Homologene; OrthoFinder; sonicParanoid; HGNC; NCBI; Inparanoid; orthoMCL; SwiftOrtho; eggNOG; OrthoInspector; OrthoDB; Panther; Phylome; Domainoid; TreeFam; **human-thale cress** 15 ortholog Panther; eggNOG; Phylome; TreeFam; OMA; Hieranoid; sonicParanoid; Homologene; Inparanoid; SwiftOrtho; OrthoInspector; OrthoFinder; OrthoDB; Domainoid; orthoMCL; **human-worm** 18 ortholog OrthoFinder; Hieranoid; Compara; OrthoInspector; orthoMCL; eggNOG; OMA; sonicParanoid; OrthoDB; Isobase; Domainoid; Panther; Homologene; Phylome; Inparanoid; RoundUp; TreeFam; SwiftOrtho; **mosquito-mouse** 14 ortholog OrthoDB; OrthoFinder; Homologene; Domainoid; Panther; OrthoInspector; Inparanoid; Phylome; SwiftOrtho; TreeFam; eggNOG; OMA; Hieranoid; sonicParanoid; **mosquito-rat** 14 ortholog OrthoInspector; Panther; OMA; Phylome; TreeFam; Domainoid; Homologene; sonicParanoid; OrthoFinder; Inparanoid; Hieranoid; SwiftOrtho; eggNOG; OrthoDB; **mosquito-thale cress** 14 ortholog SwiftOrtho; OrthoDB; Panther; sonicParanoid; Phylome; Domainoid; OMA; TreeFam; eggNOG; Hieranoid; Homologene; OrthoInspector; Inparanoid; OrthoFinder; **mosquito-worm** 14 ortholog eggNOG; Phylome; Homologene; TreeFam; OrthoInspector; Domainoid; OrthoFinder; Inparanoid; SwiftOrtho; Hieranoid; sonicParanoid; OMA; OrthoDB; Panther; **mouse-rat** 16 ortholog Compara; OMA; OrthoFinder; Homologene; Domainoid; Inparanoid; OrthoInspector; SwiftOrtho; eggNOG; OrthoDB; sonicParanoid; orthoMCL; Hieranoid; Panther; Phylome; TreeFam; **mouse-thale cress** 15 ortholog eggNOG; OrthoInspector; Inparanoid; Panther; Domainoid; SwiftOrtho; Phylome; OMA; TreeFam; sonicParanoid; Hieranoid; OrthoFinder; orthoMCL; Homologene; OrthoDB; **mouse-worm** 18 ortholog OrthoFinder; TreeFam; Compara; Homologene; Hieranoid; OrthoInspector; Inparanoid; eggNOG; SwiftOrtho; orthoMCL; OMA; sonicParanoid; OrthoDB; Isobase; Panther; Domainoid; Phylome; RoundUp; **rat-thale cress** 15 ortholog eggNOG; Phylome; TreeFam; Homologene; OrthoFinder; Inparanoid; OrthoInspector; SwiftOrtho; orthoMCL; sonicParanoid; Domainoid; OMA; OrthoDB; Hieranoid; Panther; **rat-worm** 16 ortholog OMA; Domainoid; eggNOG; Homologene; OrthoFinder; OrthoDB; OrthoInspector; Inparanoid; SwiftOrtho; Hieranoid; sonicParanoid; Panther; Phylome; TreeFam; Compara; orthoMCL; **thale cress-worm** 15 ortholog Phylome; orthoMCL; TreeFam; Homologene; sonicParanoid; Domainoid; eggNOG; Inparanoid; SwiftOrtho; OMA; OrthoFinder; OrthoInspector; Hieranoid; OrthoDB; Panther; **bacteria-bacteria** 11 paralog Inparanoid; SwiftOrtho; Panther; orthoMCL; Phylome; sonicParanoid; Domainoid; OrthoFinder; OMA; OrthoInspector; eggNOG; **baker's yeast-baker's yeast** 15 paralog Compara; Domainoid; eggNOG; sonicParanoid; Homologene; Isobase; Inparanoid; Panther; Phylome; OrthoInspector; OrthoFinder; RoundUp; OMA; SGD; orthoMCL; **fish-fish** 15 paralog Inparanoid; OrthoDB; SwiftOrtho; orthoMCL; Panther; Phylome; RoundUp; OrthoFinder; Domainoid; sonicParanoid; Compara; OrthoInspector; OMA; eggNOG; Homologene; **fission yeast-fission yeast** 12 paralog Homologene; Inparanoid; Panther; eggNOG; Phylome; OMA; RoundUp; OrthoInspector; sonicParanoid; OrthoFinder; Domainoid; orthoMCL; **fly-fly** 15 paralog Domainoid; OMA; OrthoDB; Isobase; Homologene; Panther; OrthoInspector; Phylome; Inparanoid; RoundUp; eggNOG; Compara; OrthoFinder; sonicParanoid; orthoMCL; **frog-frog** 14 paralog Inparanoid; sonicParanoid; SwiftOrtho; OrthoDB; Domainoid; Panther; Phylome; eggNOG; RoundUp; Compara; OrthoFinder; OrthoInspector; OMA; Homologene; **human-human** 16 paralog Compara; OrthoFinder; orthoMCL; OrthoInspector; eggNOG; OMA; Domainoid; OrthoDB; Homologene; Isobase; Inparanoid; Panther; sonicParanoid; SwiftOrtho; Phylome; RoundUp; **mosquito-mosquito** 11 paralog Panther; Phylome; OMA; Homologene; OrthoFinder; Inparanoid; OrthoInspector; eggNOG; sonicParanoid; Domainoid; OrthoDB; **mouse-mouse** 17 paralog OrthoInspector; OrthoFinder; sonicParanoid; orthoMCL; OrthoDB; Isobase; Panther; HGNC; Homologene; Phylome; RoundUp; Inparanoid; SwiftOrtho; Compara; Domainoid; eggNOG; OMA; **rat-rat** 15 paralog orthoMCL; OrthoDB; HGNC; OrthoFinder; Panther; Phylome; eggNOG; Compara; Domainoid; OrthoInspector; OMA; Homologene; sonicParanoid; Inparanoid; SwiftOrtho; **thale cress-thale cress** 13 paralog Inparanoid; sonicParanoid; SwiftOrtho; OrthoDB; OMA; OrthoInspector; Panther; OrthoFinder; Phylome; Domainoid; orthoMCL; eggNOG; Homologene; **worm-worm** 16 paralog Homologene; Inparanoid; OrthoInspector; SwiftOrtho; orthoMCL; OrthoDB; Isobase; eggNOG; Domainoid; Panther; sonicParanoid; Phylome; RoundUp; OrthoFinder; Compara; OMA; ## Table 4. DIOPT Weights DIOPT weights were calculated based on the mean semantic similarity of high quality GO molecular function annotation of all fly-human orthologous pairs predicted by each tool from DIOPT vs1. As such, they do not predict overall performance of an algorithm. Please go to the DIOPT publication for detailed information (). Sort **Prediction Method** **DIOPT Weight** **Compara** 0.93 **Domainoid** 1 **ECGA** 1.5 **eggNOG** 0.9 **HGNC** 1.5 **Hieranoid** 1 **Homologene** 1 **Inparanoid** 1.05 **Isobase** 0.95 **OMA** 1.01 **OrthoDB** 1.01 **OrthoFinder** 1 **OrthoInspector** 1 **orthoMCL** 0.9 **Panther** 1.1 **Phylome** 0.91 **RoundUp** 1.03 **SGD** 1.5 **sonicParanoid** 1 **TreeFam** 0.96 **ZFIN** 1.5 **NCBI** 1 **SwiftOrtho** 1 ## DIOPT Score Distributions ### Ortholog Score Distribution (version 9) ![DIOPT 9 ortholog distribution graph](/sites/g/files/omnuum5366/files/fly/files/diopt9-1_ortholog_score_distribution.png) ### Paralog Score Distribution (version 9) ![DIOPT 9 paralog distribution graph](/sites/g/files/omnuum5366/files/fly/files/diopt9-1_paralog_score_distribution.png) ## DIOPT API You can access diopt data through an API call. For details see: ## Diopt Versions 9.1 Oct 2021 - added 2 prediction algorithms (NCBI, Domainoid) 9.0 Sept 2021 - - added 2 species: Mosquito (Anopheles gambiae) and E. coli - added 2 sources of annotation (SGD and ECOCYC) - added 2 prediction algorithms (sonicParanoid and Domainoid) 8.5- Aug 2021 - - updated UI 8.0- Aug 2019 - - Updated [Data Sources](/diopt-documentation) 7.1- Mar 2018 - - Allow user to submit missing relationships - Allow user to add feedback 7.0- Jan 2018 - - Updated [Data Sources](/diopt-documentation) - added 3 new algorithms: OrthoFinder, OrthoInspector, Hieranoid as a sources - added new species: Arabidopsis (Thale Cress) 6.0- Dec 2016 - - Updated Data Sources - added eggNOG as a source - Added paralogs 5.5- Oct 2016 - Added multi-sequence alignment from target "All" heatmap 5.4- Sept 2016 - Added target species "All" and new filter 5.3- May 2016 - Added more prediction tools (Panther, HGNC and ZFIN) 5.2.1- April 2016 - Added orthologous rank **High**: best score both ways AND DIOPT score >=2 **Moderate**: (best score forward or reverse) AND DIOPT score >=2 *or* DIOPT score >=4 **Low**: all others 5.2- April 2016 - Added New Spcecies (Rattus norvegicus) 5.1.1 - December 2015 - Added Best forward and reverse columns 5.1 - November 2015 - Upgraded gene matching algorithm 5.0 - November 2015 - Upgraded data sources to version 5