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Phenotype Ontology
Like Gene Ontology (GO), phenotypy ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Phenotype ontologies we have incorporated are as follows:

• Disease Ontology (DO) Ontology (DO)
  DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
  
• Human Phenotype (HP) Ontology (HP)
  HP captures phenotypic abnormalities that are described in OMIM, along with the corresponding disease-causing genes. It includes three complementary biological concepts: Mode_of_Inheritance (MI), ONset_and_clinical_course (ON), and Phenotypic_Abnormality (PA).
  
• Mouse Phenotype (MP) Ontology (MP)
  MP describes phenotypes of the mouse after a specific gene is genetically disrupted. Using it, Mouse Genome Informatics (MGI) provides high-coverate gene-level phenotypes for the mouse.
  
• Worm Phenotype (WP) Ontology (WP)
  WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
  
• Yeast Phenotype (YP) Ontology (YP)
  Based on YP which is the major contributor to the Ascomycete phenotype ontology, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
  
• Fly Phenotype (FP) Ontology (FP)
  FP refers to FlyBase controlled vocabulary. Specifically, a structured controlled vocabulary is used for the annotation of alleles (for their mutagen etc) in FlyBase.
  
• Fly Anatomy (FA) Ontology (FA)
  FA is a structured controlled vocabulary of the anatomy of Drosophila melanogaster, used for the description of phenotypes and where a gene is expressed.
  
• Zebrafish Anatomy (ZA) Ontology (ZA)
  ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
  
• Xenopus Anatomy (XA) Ontology (XA)
  XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
  
• Arabidopsis Plant Ontology (AP) Ontology (AP)
  As a major contributor to Plant Ontology which describes plant anatomical and morphological structures (AN) and growth and developmental stages (DE), the Arabidopsis Information Resource (TAIR) provides arabidopsis plant ontology annotations for the model higher plant Arabidopsis thaliana.
  
• Enzyme Commission (EC) Ontology (EC)
  Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed.
  
• DrugBank ATC (DB) Ontology (DB)
  In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
  
• UniProtKB KeyWords (KW) Ontology (KW)
  Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
  
• UniProtKB UniPathway (UP) Ontology (UP)
  UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.
  

Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

• Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
  
• Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations:
  For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).
  

Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.

• Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
  
• Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations:
  For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).
  

Superfamily domains annotated to this ZA term (SDZA level: Least Informative)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
DUSP-like	0	DIRECT
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	DIRECT
SMAD MH1 domain	0	DIRECT
Aquaporin-like	0	DIRECT
Retrovirus zinc finger-like domains	0	DIRECT
Smc hinge domain	0	DIRECT
Moesin tail domain	0	DIRECT
ADC-like	0	DIRECT
Connexin43	0	DIRECT
Cap-Gly domain	0	DIRECT
CRAL/TRIO N-terminal domain	0	DIRECT
Tubulin nucleotide-binding domain-like	0	DIRECT
p53 tetramerization domain	0	DIRECT
Heat shock protein 70kD (HSP70), peptide-binding domain	0	DIRECT
Translation proteins	0	DIRECT
Kazal-type serine protease inhibitors	0	DIRECT
Class II aaRS ABD-related	0	DIRECT
Class II aaRS and biotin synthetases	0	DIRECT
LDL receptor-like module	0	DIRECT
Rhodanese/Cell cycle control phosphatase	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Translation proteins SH3-like domain	0	DIRECT
Translational machinery components	0	DIRECT
Single hybrid motif	0	DIRECT
TATA-box binding protein-like	0	DIRECT
Nuclear receptor coactivator interlocking domain	0	DIRECT
LCCL domain	0	DIRECT
Lipovitellin-phosvitin complex, superhelical domain	0	DIRECT
CCCH zinc finger	0	DIRECT
BRK domain-like	0	DIRECT
ENTH/VHS domain	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Sec7 domain	0	DIRECT
Tricorn protease domain 2	0	DIRECT
ACT-like	0	DIRECT
BPTI-like	0	DIRECT
Cullin repeat-like	0	DIRECT
Polo-box domain	0	DIRECT
Arginase/deacetylase	0	DIRECT
Metallo-dependent hydrolases	0	DIRECT
Aldolase	0	DIRECT
SNARE-like	0	DIRECT
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains	0	DIRECT
Glutathione synthetase ATP-binding domain-like	0	DIRECT
Tubulin C-terminal domain-like	0	DIRECT
CalX-like	0	DIRECT
Composite domain of metallo-dependent hydrolases	0	DIRECT
Class I glutamine amidotransferase-like	0	DIRECT
Nucleotide cyclase	0	DIRECT
Notch domain	0	DIRECT
Lipovitellin-phosvitin complex; beta-sheet shell regions	0	DIRECT
HCP-like	0	DIRECT
DNase I-like	0	DIRECT
HSP20-like chaperones	0	DIRECT
Cysteine proteinases	0.0007718	DIRECT
Protein kinase-like (PK-like)	0.08056	INHERITED FROM: dermal superficial region || dermis || scale
FnI-like domain	0.1431	INHERITED FROM: palatoquadrate arch || paired fin || pectoral fin || ventral fin fold || palatoquadrate cartilage
Nucleotide-diphospho-sugar transferases	0.1752	INHERITED FROM: pectoral fin fold
WD40 repeat-like	0.263	INHERITED FROM: photoreceptor outer segment layer || retinal outer nuclear layer
Alkaline phosphatase-like	0.2862	INHERITED FROM: pharyngeal arch 2 || ceratohyal cartilage || ventral hyoid arch || pharyngeal arch 2 skeleton
Cytokine	0.3058	INHERITED FROM: dermatocranium || olfactory region || paired fin || pectoral fin || fin bud
NAD(P)-binding Rossmann-fold domains	0.3738	INHERITED FROM: retinal outer plexiform layer || retinal inner plexiform layer
Multidrug efflux transporter AcrB transmembrane domain	0.4496	INHERITED FROM: hyosymplectic cartilage || retinal ganglion cell layer || dorsal hyoid arch
L domain-like	0.6483	INHERITED FROM: dermal superficial region || dermis || scale
Concanavalin A-like lectins/glucanases	0.9103	INHERITED FROM: epidermis

Family domains annotated to this ZA term (SDZA level: Least Informative)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
p53 tetramerization domain	0	DIRECT
Elongation factors	0	DIRECT
PWWP domain	0	DIRECT
Platelet-derived growth factor-like	0	DIRECT
CRAL/TRIO domain	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Hydantoinase (dihydropyrimidinase)	0	DIRECT
Retrovirus zinc finger-like domains	0	DIRECT
Sec7 domain	0	DIRECT
Aquaporin-like	0	DIRECT
Nitrogenase iron protein-like	0	DIRECT
Class I glutamine amidotransferases (GAT)	0	DIRECT
Biotinyl/lipoyl-carrier proteins and domains	0	DIRECT
FYVE, a phosphatidylinositol-3-phosphate binding domain	0	DIRECT
CalX-beta domain	0	DIRECT
LDL receptor-like module	0	DIRECT
V set domains (antibody variable domain-like)	0	DIRECT
Clathrin coat assembly domain	0	DIRECT
Adenylyl and guanylyl cyclase catalytic domain	0	DIRECT
Small Kunitz-type inhibitors & BPTI-like toxins	0	DIRECT
Lipovitellin-phosvitin complex; beta-sheet shell regions	0	DIRECT
Plakophilin 1 helical region	0	DIRECT
Cap-Gly domain	0	DIRECT
C5 cytosine-specific DNA methylase, DCM	0	DIRECT
Cell cycle control phosphatase, catalytic domain	0	DIRECT
Histone deacetylase, HDAC	0	DIRECT
Tubulin, GTPase domain	0	DIRECT
RUNT domain	0	DIRECT
Noncollagenous (NC1) domain of collagen IV	0	DIRECT
CCCH zinc finger	0	DIRECT
Phenylalanine metabolism regulatory domain	0	DIRECT
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains	0	DIRECT
Tubulin, C-terminal domain	0	DIRECT
LCCL domain	0	DIRECT
Connexin43	0	DIRECT
Anticodon-binding domain of Class II aaRS	0	DIRECT
Proprotein convertase P-domain	0	DIRECT
p53 DNA-binding domain-like	0	DIRECT
Extracellular domain of cell surface receptors	0	DIRECT
CRAL/TRIO N-terminal domain	0	DIRECT
SMAD MH1 domain	0	DIRECT
SMAD domain	0	DIRECT
Heat shock protein 70kD (HSP70), peptide-binding domain	0	DIRECT
Nuclear receptor coactivator interlocking domain	0	DIRECT
Zf-UBP	0	DIRECT
Chromo domain	0	DIRECT
Smc hinge domain	0	DIRECT
Hydantoinase (dihydropyrimidinase), catalytic domain	0	DIRECT
Moesin tail domain	0	DIRECT
DUSP, domain in ubiquitin-specific proteases	0	DIRECT
Myotubularin-like phosphatases	0	DIRECT
Prohormone convertase 1 pro-domain	0	DIRECT
Ubiquitin-related	0	DIRECT
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain	0	DIRECT
Notch domain	0	DIRECT
Cdc48 N-terminal domain-like	0	DIRECT
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	DIRECT
Ovomucoid domain III-like	0	DIRECT
Single strand DNA-binding domain, SSB	0	DIRECT
Lipovitellin-phosvitin complex, superhelical domain	0	DIRECT
BRK domain-like	0	DIRECT
HMG-box	0.000965	DIRECT
Ubiquitin carboxyl-terminal hydrolase, UCH	0.001283	INHERITED FROM: post-vent region || neurocranium || ventral mandibular arch || mandibular arch skeleton || splanchnocranium || olfactory region || caudal fin upper lobe || pharyngeal arch 1 || cranial cartilage || ethmoid cartilage || caudal fin lower lobe || pharyngeal arch cartilage || chondrocranium || somite
T-box	0.02243	INHERITED FROM: surface structure
Protein kinases, catalytic subunit	0.07969	INHERITED FROM: dermal superficial region || dermis || scale || dorsal longitudinal anastomotic vessel
Tetratricopeptide repeat (TPR)	0.2104	INHERITED FROM: retinal rod cell
WD40-repeat	0.2422	INHERITED FROM: photoreceptor outer segment layer || retinal cone cell
Short-chain cytokines	0.253	INHERITED FROM: integument
Multidrug efflux transporter AcrB transmembrane domain	0.253	INHERITED FROM: hyosymplectic cartilage || suspensorium || retinal ganglion cell layer || pharyngeal arch 2 || dorsal hyoid arch || ventral hyoid arch || pharyngeal arch 2 skeleton
Fibroblast growth factors (FGF)	0.2715	INHERITED FROM: dermatocranium || olfactory region || paired fin || pectoral fin || fin bud
VWC domain	0.2715	INHERITED FROM: median fin fold || ventral fin fold
Motor proteins	0.6914	INHERITED FROM: photoreceptor outer segment layer

Trees by TreeVector

A presence/absence matrix is generated using protein domain architecture data for all genomes in SUPERFAMILY. The PAUP software is used to produce a single, large tree topology using heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as if individual trees had been produced. However, this data is extracted from the single large tree. This produces a higher quality topology than if the trees had been produced on their own, and allows the trees to be displayed instantly.

Supra-domains annotated to this ZA term (SPZA level: Least Informative)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Retrovirus zinc finger-like domains	0	DIRECT
HSP20-like chaperones	0	DIRECT
LDL receptor-like module	0	DIRECT
SMAD MH1 domain	0	DIRECT
BRK domain-like	0	DIRECT
Smc hinge domain	0	DIRECT
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains	0	DIRECT
Moesin tail domain	0	DIRECT
Translational machinery components	0	DIRECT
ENTH/VHS domain	0	DIRECT
Kazal-type serine protease inhibitors	0	DIRECT
BPTI-like	0	DIRECT
Arginase/deacetylase	0	DIRECT
DNase I-like	0	DIRECT
Aquaporin-like	0	DIRECT
Heat shock protein 70kD (HSP70), peptide-binding domain	0	DIRECT
CalX-like	0	DIRECT
Translation proteins SH3-like domain	0	DIRECT
HCP-like	0	DIRECT
DUSP-like	0	DIRECT
Single hybrid motif	0	DIRECT
TATA-box binding protein-like	0	DIRECT
SNARE-like	0	DIRECT
ADC-like	0	DIRECT
CCCH zinc finger	0	DIRECT
Tubulin C-terminal domain-like	0	DIRECT
ACT-like	0	DIRECT
Nucleotide cyclase	0	DIRECT
Tricorn protease domain 2	0	DIRECT
Composite domain of metallo-dependent hydrolases	0	DIRECT
Cullin repeat-like	0	DIRECT
p53 tetramerization domain	0	DIRECT
Class II aaRS ABD-related	0	DIRECT
Lipovitellin-phosvitin complex; beta-sheet shell regions	0	DIRECT
Cap-Gly domain	0	DIRECT
Glutathione synthetase ATP-binding domain-like	0	DIRECT
Translation proteins	0	DIRECT
Notch domain	0	DIRECT
Polo-box domain	0	DIRECT
Class I glutamine amidotransferase-like	0	DIRECT
Lipovitellin-phosvitin complex, superhelical domain	0	DIRECT
Class II aaRS and biotin synthetases	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Aldolase	0	DIRECT
Tubulin nucleotide-binding domain-like	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Metallo-dependent hydrolases	0	DIRECT
Rhodanese/Cell cycle control phosphatase	0	DIRECT
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	DIRECT
CRAL/TRIO N-terminal domain	0	DIRECT
Sec7 domain	0	DIRECT
Nuclear receptor coactivator interlocking domain	0	DIRECT
LCCL domain	0	DIRECT
Connexin43	0	DIRECT
Cysteine proteinases	0.0004699	DIRECT
Growth factor receptor domain	0.0008415	DIRECT
HMG-box	0.0009554	DIRECT
vWA-like	0.03717	INHERITED FROM: epidermis
Protein kinase-like (PK-like)	0.06282	INHERITED FROM: dermis || scale || dermal superficial region || intersegmental vein
FnI-like domain	0.1186	INHERITED FROM: pectoral fin || palatoquadrate cartilage || palatoquadrate arch || ventral fin fold || paired fin
Nucleotide-diphospho-sugar transferases	0.148	INHERITED FROM: pectoral fin fold
Cystine-knot cytokines	0.1883	INHERITED FROM: cranial blood vessel
WD40 repeat-like	0.2313	INHERITED FROM: eye || retinal photoreceptor layer || retinal outer nuclear layer || photoreceptor outer segment layer
Alkaline phosphatase-like	0.2539	INHERITED FROM: ceratohyal cartilage || pharyngeal arch 2 || pharyngeal arch 2 skeleton || ventral hyoid arch
Cytokine	0.2734	INHERITED FROM: dermatocranium || pectoral fin || olfactory region || fin bud || chondrocranium || paired fin
NAD(P)-binding Rossmann-fold domains	0.3391	INHERITED FROM: retinal inner plexiform layer || retinal outer plexiform layer
UBA-like	0.3881	INHERITED FROM: ethmoid cartilage
Multidrug efflux transporter AcrB transmembrane domain	0.4156	INHERITED FROM: dorsal hyoid arch || hyosymplectic cartilage || suspensorium || retinal ganglion cell layer
L domain-like	0.621	INHERITED FROM: dermis || scale || dermal superficial region
Immunoglobulin	0.763	INHERITED FROM: scale
Concanavalin A-like lectins/glucanases	0.9023	INHERITED FROM: epidermis

Supra-domains annotated to this ZA term (SPZA level: Least Informative)
Highlighted in gray are those with FDR>0.001

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module	0	DIRECT
55550,55550 55550 - SH2 domain 55550 - SH2 domain	0	DIRECT
48425,50729 48425 - Sec7 domain 50729 - PH domain-like	0	DIRECT
52058,49265 52058 - L domain-like 49265 - Fibronectin type III	0	DIRECT
54160,54160 54160 - Chromo domain-like 54160 - Chromo domain-like	0	DIRECT
56968,48431 56968 - Lipovitellin-phosvitin complex; beta-sheet shell regions 48431 - Lipovitellin-phosvitin complex, superhelical domain	0	DIRECT
81324,81324 81324 - Voltage-gated potassium channels 81324 - Voltage-gated potassium channels	0	DIRECT
49785,57184 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain	0	DIRECT
50729,47473 50729 - PH domain-like 47473 - EF-hand	0	DIRECT
90193,90193 90193 - Notch domain 90193 - Notch domain	0	DIRECT
47473,51695 47473 - EF-hand 51695 - PLC-like phosphodiesterases	0	DIRECT
57362,57362 57362 - BPTI-like 57362 - BPTI-like	0	DIRECT
46785,46785 46785 - "Winged helix" DNA-binding domain 46785 - "Winged helix" DNA-binding domain	0	DIRECT
57196,63825 57196 - EGF/Laminin 63825 - YWTD domain	0	DIRECT
141072,141072 141072 - CalX-like 141072 - CalX-like	0	DIRECT
53300,53300 53300 - vWA-like 53300 - vWA-like	0	DIRECT
46938,52087 46938 - CRAL/TRIO N-terminal domain 52087 - CRAL/TRIO domain	0	DIRECT
55021,56534 55021 - ACT-like 56534 - Aromatic aminoacid monoxygenases, catalytic and oligomerization domains	0	DIRECT
57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0	DIRECT
57196,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
57903,47370 57903 - FYVE/PHD zinc finger 47370 - Bromodomain	0	DIRECT
53067,100920 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain	0	DIRECT
57184,57603 57184 - Growth factor receptor domain 57603 - FnI-like domain	0	DIRECT
54001,143791 54001 - Cysteine proteinases 143791 - DUSP-like	0	DIRECT
50978,50998 50978 - WD40 repeat-like 50998 - Quinoprotein alcohol dehydrogenase-like	0	DIRECT
50156,50044 50156 - PDZ domain-like 50044 - SH3-domain	0	DIRECT
54791,54791 54791 - Eukaryotic type KH-domain (KH-domain type I) 54791 - Eukaryotic type KH-domain (KH-domain type I)	0	DIRECT
52743,49785 52743 - Subtilisin-like 49785 - Galactose-binding domain-like	0	DIRECT
50447,50465 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	DIRECT
54585,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
52540,50447 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins	0	DIRECT
51556,51338 51556 - Metallo-dependent hydrolases 51338 - Composite domain of metallo-dependent hydrolases	0	DIRECT
90257,57997 90257 - Myosin rod fragments 57997 - Tropomyosin	0	DIRECT
63825,57196 63825 - YWTD domain 57196 - EGF/Laminin	0	DIRECT
57196,90193 57196 - EGF/Laminin 90193 - Notch domain	0	DIRECT
49854,57196 49854 - Spermadhesin, CUB domain 57196 - EGF/Laminin	0	DIRECT
50692,54585 50692 - ADC-like 54585 - Cdc48 domain 2-like	0	DIRECT
49417,47719 49417 - p53-like transcription factors 47719 - p53 tetramerization domain	0	DIRECT
57850,57850 57850 - RING/U-box 57850 - RING/U-box	0	DIRECT
52490,55307 52490 - Tubulin nucleotide-binding domain-like 55307 - Tubulin C-terminal domain-like	0	DIRECT
57903,57903 57903 - FYVE/PHD zinc finger 57903 - FYVE/PHD zinc finger	0	DIRECT
50729,56112 50729 - PH domain-like 56112 - Protein kinase-like (PK-like)	0	DIRECT
48452,81901 48452 - TPR-like 81901 - HCP-like	0	DIRECT
54160,52540 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
57440,57440 57440 - Kringle-like 57440 - Kringle-like	0.3359	INHERITED FROM: pharyngeal arch 1
57196,49854 57196 - EGF/Laminin 49854 - Spermadhesin, CUB domain	0.3359	INHERITED FROM: fin
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like	0.641	INHERITED FROM: retinal ganglion cell layer
50156,50156 50156 - PDZ domain-like 50156 - PDZ domain-like	0.705	INHERITED FROM: eye photoreceptor cell || retinal outer nuclear layer

Supra-domains annotated to this ZA term (SPZA level: Least Informative)
Highlighted in gray are those with FDR>0.001

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
50729,47473,51695 50729 - PH domain-like 47473 - EF-hand 51695 - PLC-like phosphodiesterases	0	DIRECT
57196,63825,57196 57196 - EGF/Laminin 63825 - YWTD domain 57196 - EGF/Laminin	0	DIRECT
52540,50447,50465 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	0	DIRECT
57196,57184,57196 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0	DIRECT
57184,57184,57196 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57196 - EGF/Laminin	0	DIRECT
53067,53067,100920 53067 - Actin-like ATPase domain 53067 - Actin-like ATPase domain 100920 - Heat shock protein 70kD (HSP70), peptide-binding domain	0	DIRECT
57196,49899,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
54160,52540,52540 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
54585,52540,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
49854,57196,49854 49854 - Spermadhesin, CUB domain 57196 - EGF/Laminin 49854 - Spermadhesin, CUB domain	0	DIRECT
57196,57196,90193 57196 - EGF/Laminin 57196 - EGF/Laminin 90193 - Notch domain	0	DIRECT
90193,90193,90193 90193 - Notch domain 90193 - Notch domain 90193 - Notch domain	0	DIRECT
54160,54160,52540 54160 - Chromo domain-like 54160 - Chromo domain-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
57196,57184,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0	DIRECT
52743,49785,57184 52743 - Subtilisin-like 49785 - Galactose-binding domain-like 57184 - Growth factor receptor domain	0	DIRECT
57184,57184,57184 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain 57184 - Growth factor receptor domain	0	DIRECT
50156,50044,52540 50156 - PDZ domain-like 50044 - SH3-domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
54897,52743,49785 54897 - Protease propeptides/inhibitors 52743 - Subtilisin-like 49785 - Galactose-binding domain-like	0	DIRECT
57850,57850,57850 57850 - RING/U-box 57850 - RING/U-box 57850 - RING/U-box	0	DIRECT
50692,54585,52540 50692 - ADC-like 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
75399,75399,75399 75399 - Plakin repeat 75399 - Plakin repeat 75399 - Plakin repeat	0	DIRECT
57424,57424,57424 57424 - LDL receptor-like module 57424 - LDL receptor-like module 57424 - LDL receptor-like module	0	DIRECT
47031,50729,50729 47031 - Second domain of FERM 50729 - PH domain-like 50729 - PH domain-like	0	DIRECT
57184,52058,49265 57184 - Growth factor receptor domain 52058 - L domain-like 49265 - Fibronectin type III	0	DIRECT
57196,90193,90193 57196 - EGF/Laminin 90193 - Notch domain 90193 - Notch domain	0	DIRECT
52058,49265,49265 52058 - L domain-like 49265 - Fibronectin type III 49265 - Fibronectin type III	0	DIRECT
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like	0.5066	INHERITED FROM: retinal ganglion cell layer

Trees by TreeVector

A presence/absence matrix is generated using protein domains and supradomains for all genomes in SUPERFAMILY. The RAxML software is used to produce a single, large tree topology using heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as if individual trees had been produced. However, this data is extracted from the single large tree. This produces a higher quality topology than if the trees had been produced on their own, and allows the trees to be displayed instantly.