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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’s 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 (SPHP) 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:SPHP.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 FA term (Not in SDFA)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
Rhodanese/Cell cycle control phosphatase	0	DIRECT
SPOC domain-like	0	DIRECT
Frizzled cysteine-rich domain	0	DIRECT
NTF2-like	0	DIRECT
lambda repressor-like DNA-binding domains	0.009259	INHERITED FROM: maxillary palp sense organ || adult head sensillum || maxillary palp sensillum basiconicum || adult olfactory receptor neuron Or42a
Homeodomain-like	0.01602	INHERITED FROM: head bristle || dorsal margin photoreceptor || dorsal margin ommatidium || adult thoracic sensillum || adult mesothoracic sensillum
Cadherin-like	0.03633	INHERITED FROM: photoreceptor cell R4
EGF/Laminin	0.06316	INHERITED FROM: tertiary pigment cell || eye photoreceptor cell stalk
Second domain of FERM	0.1131	INHERITED FROM: head bristle
SH2 domain	0.2203	INHERITED FROM: ommatidium
HLH, helix-loop-helix DNA-binding domain	0.3458	INHERITED FROM: anterior orbital bristle || microchaeta
Growth factor receptor domain	0.3703	INHERITED FROM: photoreceptor cell R7
Ankyrin repeat	0.4399	INHERITED FROM: Johnston organ neuron || Johnston organ
Fibronectin type III	0.5533	INHERITED FROM: prothoracic leg taste bristle || prothoracic leg taste bristle chemosensory neuron || leg taste bristle || prothoracic leg sensillum
Protein kinase-like (PK-like)	0.5654	INHERITED FROM: photoreceptor cell R8 of pale ommatidium
Immunoglobulin	0.9641	INHERITED FROM: prothoracic leg taste bristle || leg taste bristle

Family domains annotated to this FA term (SDFA level: Moderately Informative)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
Dual specificity phosphatase-like	0	DIRECT
Diacylglycerol kinase-like	0	DIRECT
Cell cycle control phosphatase, catalytic domain	0	DIRECT
Exostosin	0	DIRECT
NTF2-like	0	DIRECT
Frizzled cysteine-rich domain	0	DIRECT
PLC-like (P variant)	0	DIRECT
Cdc48 N-terminal domain-like	0	DIRECT
Laminin G-like module	0.0001665	DIRECT
Homeodomain	0.005547	INHERITED FROM: head bristle || dorsal margin photoreceptor || dorsal margin ommatidium || adult mesothoracic sensillum
POU-specific domain	0.01832	INHERITED FROM: maxillary palp sense organ || maxillary palp sensillum basiconicum || adult olfactory receptor neuron Or42a
Cadherin	0.0619	INHERITED FROM: outer photoreceptor cell || photoreceptor cell R4
Second domain of FERM	0.09677	INHERITED FROM: head bristle
Armadillo repeat	0.1123	INHERITED FROM: microchaeta
Growth factor receptor domain	0.1377	INHERITED FROM: dorsocentral bristle
Rel/Dorsal transcription factors, DNA-binding domain	0.1795	INHERITED FROM: dorsocentral bristle
EGF-type module	0.185	INHERITED FROM: tertiary pigment cell || secondary pigment cell
SH2 domain	0.2073	INHERITED FROM: photoreceptor cell R7 || ommatidium
I set domains	0.3188	INHERITED FROM: prothoracic leg taste bristle || inner photoreceptor cell || prothoracic leg taste bristle chemosensory neuron || leg taste bristle || prothoracic leg sensillum
HLH, helix-loop-helix DNA-binding domain	0.3425	INHERITED FROM: anterior orbital bristle || microchaeta
Ankyrin repeat	0.4341	INHERITED FROM: Johnston organ neuron || Johnston organ || adult antennal sense organ
Fibronectin type III	0.5591	INHERITED FROM: prothoracic leg taste bristle || prothoracic leg taste bristle chemosensory neuron || leg taste bristle || prothoracic leg sensillum
Protein kinases, catalytic subunit	0.6254	INHERITED FROM: photoreceptor cell R8 of pale ommatidium

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 FA term (Not in SPFA)
Highlighted in gray are those with FDR>0.001

Supra-domain (Single)	FDR (all)	Annotation (direct or inherited)
Frizzled cysteine-rich domain	0	DIRECT
NTF2-like	0	DIRECT
SPOC domain-like	0	DIRECT
Rhodanese/Cell cycle control phosphatase	0	DIRECT
lambda repressor-like DNA-binding domains	0.006564	INHERITED FROM: maxillary palp sense organ || adult head sensillum || maxillary palp sensillum basiconicum || adult olfactory receptor neuron Or42a
Homeodomain-like	0.01151	INHERITED FROM: head bristle || adult sensillum || mesothoracic bristle || dorsal margin photoreceptor || dorsal margin ommatidium || adult thoracic sensillum || mesothoracic tibial apical bristle || adult mesothoracic sensillum
Cadherin-like	0.02716	INHERITED FROM: photoreceptor cell R4 || ommatidium
SMAD/FHA domain	0.04547	INHERITED FROM: ommatidium
EGF/Laminin	0.04879	INHERITED FROM: adult head sensillum || tertiary pigment cell || eye photoreceptor cell stalk || ommatidium
Second domain of FERM	0.09067	INHERITED FROM: head bristle
SAM/Pointed domain	0.1428	INHERITED FROM: photoreceptor cell R7
SH2 domain	0.1892	INHERITED FROM: photoreceptor cell R7 || ommatidium
HLH, helix-loop-helix DNA-binding domain	0.3102	INHERITED FROM: anterior orbital bristle || microchaeta
Growth factor receptor domain	0.3337	INHERITED FROM: photoreceptor cell R7 || retinal pigment cell
Ankyrin repeat	0.4027	INHERITED FROM: Johnston organ neuron || Johnston organ || adult antennal sense organ
Fibronectin type III	0.5184	INHERITED FROM: prothoracic leg taste bristle || prothoracic leg taste bristle chemosensory neuron || leg taste bristle || prothoracic leg sensillum
Protein kinase-like (PK-like)	0.5304	INHERITED FROM: photoreceptor cell R8 of pale ommatidium
Immunoglobulin	0.9546	INHERITED FROM: prothoracic leg taste bristle || leg taste bristle

Supra-domains annotated to this FA term (Not in SPFA)
Highlighted in gray are those with FDR>0.001

Supra-domain (Duplex) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
49899,57196 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin	0	DIRECT
54585,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
57196,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like	0.006564	INHERITED FROM: maxillary palp sense organ || adult head sensillum || maxillary palp sensillum basiconicum || adult olfactory receptor neuron Or42a
49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0.02872	INHERITED FROM: photoreceptor cell R4
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like	0.05316	INHERITED FROM: outer photoreceptor cell || photoreceptor cell R4
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.1107	INHERITED FROM: photoreceptor cell R7 || inner photoreceptor cell || interommatidial bristle || adult thoracic sensillum || adult mesothoracic sensillum
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.1709	INHERITED FROM: eye photoreceptor cell || tertiary pigment cell || secondary pigment cell || eye photoreceptor cell stalk
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0.1738	INHERITED FROM: dorsocentral bristle
54236,47031 54236 - Ubiquitin-like 47031 - Second domain of FERM	0.187	INHERITED FROM: head bristle
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0.2069	INHERITED FROM: dorsocentral bristle
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	0.2299	INHERITED FROM: postalar bristle
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III	0.3674	INHERITED FROM: prothoracic leg taste bristle || prothoracic leg taste bristle chemosensory neuron || leg taste bristle || prothoracic leg sensillum
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin	0.888	INHERITED FROM: prothoracic leg taste bristle || leg taste bristle

Supra-domains annotated to this FA term (Not in SPFA)
Highlighted in gray are those with FDR>0.001

Supra-domain (Triple) in N- to C-terminal order	FDR (all)	Annotation (direct or inherited)
54585,52540,52540 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
57196,49899,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
50692,54585,52540 50692 - ADC-like 54585 - Cdc48 domain 2-like 52540 - P-loop containing nucleoside triphosphate hydrolases	0	DIRECT
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like	0.05316	INHERITED FROM: outer photoreceptor cell || photoreceptor cell R4
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin	0.06207	INHERITED FROM: photoreceptor cell R6 || adult head sensillum || eye photoreceptor cell || tertiary pigment cell || secondary pigment cell || photoreceptor cell R1 || eye photoreceptor cell stalk
57196,57196,57184 57196 - EGF/Laminin 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.1738	INHERITED FROM: adult thoracic sensillum || adult mesothoracic sensillum
54236,47031,50729 54236 - Ubiquitin-like 47031 - Second domain of FERM 50729 - PH domain-like	0.2635	INHERITED FROM: head bristle
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III	0.4456	INHERITED FROM: prothoracic leg taste bristle || prothoracic leg taste bristle chemosensory neuron || leg taste bristle || prothoracic leg sensillum
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.5035	INHERITED FROM: prothoracic leg taste bristle || leg taste bristle

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.