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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 FA term (Not in SDFA)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
Integrin alpha N-terminal domain	0	DIRECT
NAD kinase/diacylglycerol kinase-like	0	DIRECT
Rhodanese/Cell cycle control phosphatase	0	DIRECT
YVTN repeat-like/Quinoprotein amine dehydrogenase	0	DIRECT
MIR domain	0	DIRECT
Terpenoid synthases	0	DIRECT
Cullin homology domain	0	DIRECT
Sema domain	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
Mob1/phocein	0	DIRECT
Tubulin C-terminal domain-like	0	DIRECT
Ferritin-like	0	DIRECT
Ribosomal protein S5 domain 2-like	0	DIRECT
Smc hinge domain	0	DIRECT
ADC-like	0	DIRECT
t-snare proteins	0	DIRECT
Plexin repeat	0	DIRECT
Cytokine	0	DIRECT
Metallo-hydrolase/oxidoreductase	0	DIRECT
Prefoldin	0	DIRECT
Translation proteins	0	DIRECT
RCC1/BLIP-II	0	DIRECT
Arginase/deacetylase	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
TIMP-like	0	DIRECT
Integrin domains	0	DIRECT
GINS helical bundle-like	0	DIRECT
B-box zinc-binding domain	0	DIRECT
WWE domain	0	DIRECT
YWTD domain	0	DIRECT
post-AAA+ oligomerization domain-like	0	DIRECT
SMAD MH1 domain	0	DIRECT
NHL repeat	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Acetyl-CoA synthetase-like	0	DIRECT
PapD-like	0	DIRECT
Cullin repeat-like	0	DIRECT
SAP domain	0	DIRECT
CAD & PB1 domains	0	DIRECT
Class II aaRS ABD-related	0	DIRECT
Tropomyosin	0	DIRECT
Tubulin nucleotide-binding domain-like	0	DIRECT
PriA/YqbF domain	0	DIRECT
alpha-catenin/vinculin-like	0	DIRECT
Aminoacid dehydrogenase-like, N-terminal domain	0	DIRECT
Snake toxin-like	0	DIRECT
RNase III domain-like	0	DIRECT
Metal cation-transporting ATPase, ATP-binding domain N	0	DIRECT
Frizzled cysteine-rich domain	0	DIRECT
RING/U-box	0.03101	INHERITED FROM: embryonic/larval garland cell || garland cell
dsRNA-binding domain-like	0.05523	INHERITED FROM: uniglomerular antennal lobe projection neuron || persistent antennal lobe projection neuron || antennal lobe projection neuron adPN || mushroom body extrinsic neuron || mushroom body intrinsic neuron || Kenyon cell || alpha/beta Kenyon cell || antennal lobe projection neuron iPN || unilateral ACT relay interneuron || BAmv3 lineage neuron || cholinergic neuron
EGF/Laminin	0.06824	INHERITED FROM: pigment cell || nephrocyte || embryonic/larval somatic muscle || abdominal 6 acute muscle || tendon cell || head mesoderm derived embryonic hemocyte || abdominal 2 acute muscle || abdominal 3 acute muscle || hub cell || embryonic precursor cell of adult midgut || abdominal 7 acute muscle || embryonic/larval midgut cell || eye photoreceptor cell stalk || abdominal 4 acute muscle || syncytium || abdominal 5 acute muscle || ventral longitudinal muscle || pericardial cell
p53-like transcription factors	0.08601	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte
Ankyrin repeat	0.09265	INHERITED FROM: Johnston organ neuron
Spectrin repeat	0.1166	INHERITED FROM: copper cell || midgut enterocyte || enterocyte
Calponin-homology domain, CH-domain	0.1294	INHERITED FROM: skeletal muscle of mesothorax || indirect flight muscle || flight muscle || skeletal muscle of thorax
Protein kinase-like (PK-like)	0.1582	INHERITED FROM: photoreceptor cell R8 of pale ommatidium || epithelial cell || intestinal stem cell
BAR/IMD domain-like	0.159	INHERITED FROM: bouton || NMJ bouton || synapse
Homeodomain-like	0.1862	INHERITED FROM: uniglomerular antennal lobe projection neuron || thoracic neuroblast || embryonic neuroblast || adult antennal lobe projection neuron VM2 adPN || adult antennal lobe projection neuron VA1v adPN || interneuron || dorsal margin photoreceptor || embryonic/larval neuron || U neuron || prothoracic ventral intersegmental muscle || syncytium || muscle cell
Immunoglobulin	0.2023	INHERITED FROM: embryonic heart cardioblast || longitudinal muscle || glial cell || prothoracic leg taste bristle chemosensory neuron || LNv neuron || adult pacemaker neuron || cardioblast || LN period neuron || pacemaker neuron || embryonic cardioblast || thoracic T1 neuron
E set domains	0.2306	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte
Transducin (alpha subunit), insertion domain	0.2408	INHERITED FROM: eo neuron
CoA-dependent acyltransferases	0.307	INHERITED FROM: skeletal muscle of mesothorax || adult somatic muscle || flight muscle || skeletal muscle of thorax
PAZ domain	0.307	INHERITED FROM: pole cell
SAM/Pointed domain	0.3357	INHERITED FROM: muscle founder cell
Cadherin-like	0.3398	INHERITED FROM: photoreceptor cell R4
L domain-like	0.3809	INHERITED FROM: BAlc1 lineage neuron
Cap-Gly domain	0.3894	INHERITED FROM: interneuron
Metalloproteases ("zincins"), catalytic domain	0.4661	INHERITED FROM: embryonic heart cardioblast || embryonic cardioblast
Fibronectin type III	0.4775	INHERITED FROM: embryonic heart cardioblast || prothoracic leg taste bristle chemosensory neuron || dendritic arborizing neuron || LNv neuron || abdominal neuron || adult pacemaker neuron || s-LNv neuron || pacemaker neuron || embryonic cardioblast || thoracic T1 neuron
Caspase-like	0.4837	INHERITED FROM: interommatidial precursor cell || peptidergic neuron || male germline cell
ENTH/VHS domain	0.4837	INHERITED FROM: imaginal disc epithelial cell
SMAD/FHA domain	0.5376	INHERITED FROM: female germline stem cell
FYVE/PHD zinc finger	0.5576	INHERITED FROM: embryonic/larval garland cell
HLH, helix-loop-helix DNA-binding domain	0.5676	INHERITED FROM: 5-6I of thorax || sensory mother cell
HAD-like	0.5728	INHERITED FROM: rhabdomere of eye photoreceptor cell
Nuclear receptor ligand-binding domain	0.6007	INHERITED FROM: adult MBp lineage neuron || mushroom body intrinsic neuron || supraesophageal ganglion neuron || interneuron
Cytochrome P450	0.7074	INHERITED FROM: midline glial cell || neuropil associated CNS glial cell || CNS glial cell || embryonic/larval glial cell
Cyclin-like	0.7194	INHERITED FROM: female germline cell
Orange domain-like	0.7752	INHERITED FROM: EG neuron || EL neuron || 5-6I of thorax
Growth factor receptor domain	0.784	INHERITED FROM: surface associated glial cell || pigment cell || RP2sib neuron || dMP2 neuron || head mesoderm derived embryonic hemocyte || hub cell || dorsal acute muscle || photoreceptor cell R7 || somatic cell of testis || retinal pigment cell || GABAergic neuron || vMP2 neuron || neuroblast NB5-2 || embryonic hemocyte || stage 1 neuroblast
SH2 domain	0.7936	INHERITED FROM: photoreceptor cell || histaminergic neuron || photoreceptor cell R7 || rhabdomeric photoreceptor cell || cyst progenitor cell || sensory organ cell || optic lobe neuron
Tetraspanin	0.8431	INHERITED FROM: sensory mother cell
beta-beta-alpha zinc fingers	1	INHERITED FROM: subesophageal ganglion neuron || serotonergic neuron

Family 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)
Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta	0	DIRECT
Integrin alpha N-terminal domain	0	DIRECT
Tubulin, GTPase domain	0	DIRECT
Mob1/phocein	0	DIRECT
Glutathione S-transferase (GST), N-terminal domain	0	DIRECT
Armadillo repeat	0	DIRECT
Cullin repeat	0	DIRECT
Kelch motif	0	DIRECT
Eps15 homology domain (EH domain)	0	DIRECT
Metal cation-transporting ATPase, ATP-binding domain N	0	DIRECT
Prefoldin	0	DIRECT
Laminin G-like module	0	DIRECT
SCF ubiquitin ligase complex WHB domain	0	DIRECT
DNA polymerase III clamp loader subunits, C-terminal domain	0	DIRECT
Arrestin/Vps26-like	0	DIRECT
SPRY domain	0	DIRECT
Histone deacetylase, HDAC	0	DIRECT
WWE domain	0	DIRECT
Aminoacid dehydrogenase-like, C-terminal domain	0	DIRECT
Nitrogenase iron protein-like	0	DIRECT
Tubulin, C-terminal domain	0	DIRECT
POU-specific domain	0	DIRECT
beta-CASP RNA-metabolising hydrolases	0	DIRECT
Cullin homology domain	0	DIRECT
MBT repeat	0	DIRECT
Plexin repeat	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Choline/Carnitine O-acyltransferase	0	DIRECT
Integrin domains	0	DIRECT
CAD domain	0	DIRECT
SAP domain	0	DIRECT
Acetyl-CoA synthetase-like	0	DIRECT
YWTD domain	0	DIRECT
MIR domain	0	DIRECT
Extracellular domain of cell surface receptors	0	DIRECT
B-box zinc-binding domain	0	DIRECT
Fibroblast growth factors (FGF)	0	DIRECT
Laminin-type module	0	DIRECT
BAR domain	0	DIRECT
Sema domain	0	DIRECT
Extended AAA-ATPase domain	0	DIRECT
Inositol polyphosphate 5-phosphatase (IPP5)	0	DIRECT
SMAD MH1 domain	0	DIRECT
RNase III catalytic domain-like	0	DIRECT
Proteasome subunits	0	DIRECT
Isoprenyl diphosphate synthases	0	DIRECT
t-snare proteins	0	DIRECT
Tetramerization domain of potassium channels	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Diacylglycerol kinase-like	0	DIRECT
Tropomyosin	0	DIRECT
NHL repeat	0	DIRECT
Group II chaperonin (CCT, TRIC), intermediate domain	0	DIRECT
2Fe-2S ferredoxin domains from multidomain proteins	0	DIRECT
MSP-like	0	DIRECT
Cell cycle control phosphatase, catalytic domain	0	DIRECT
Smc hinge domain	0	DIRECT
Anticodon-binding domain of Class II aaRS	0	DIRECT
Zf-UBP	0	DIRECT
Myb/SANT domain	0	DIRECT
Frizzled cysteine-rich domain	0	DIRECT
Ankyrin repeat	0.09145	INHERITED FROM: Johnston organ neuron || ventral multidendritic neuron
Spectrin repeat	0.1041	INHERITED FROM: oocyte || copper cell || midgut enterocyte || enterocyte
Calponin-homology domain, CH-domain	0.1184	INHERITED FROM: skeletal muscle of mesothorax || indirect flight muscle || flight muscle || skeletal muscle of thorax
PLC-like (P variant)	0.1708	INHERITED FROM: head mesoderm derived embryonic hemocyte || dorsal multidendritic neuron ddaC || dorsal multidendritic neuron || embryonic hemocyte
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.1708	INHERITED FROM: intestinal stem cell
T-box	0.1708	INHERITED FROM: embryonic/larval hypodermal muscle
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.2191	INHERITED FROM: head mesoderm derived embryonic hemocyte || lamellocyte || embryonic hemocyte
Transducin (alpha subunit), insertion domain	0.2191	INHERITED FROM: eo neuron
Protein kinases, catalytic subunit	0.2243	INHERITED FROM: photoreceptor cell R8 of pale ommatidium || intestinal stem cell
I set domains	0.2512	INHERITED FROM: embryonic heart cardioblast || abdominal sensory neuron || prothoracic leg taste bristle chemosensory neuron || dendritic arborizing neuron || mechanosensory system neuron || LNv neuron || abdominal neuron || adult pacemaker neuron || visceral muscle fiber || cardioblast || interface glial cell || s-LNv neuron || gustatory system neuron || pacemaker neuron || gustatory receptor neuron || embryonic cardioblast || thoracic T1 neuron
Pancreatic lipase, N-terminal domain	0.283	INHERITED FROM: ganglion mother cell
RecA protein-like (ATPase-domain)	0.283	INHERITED FROM: nurse cell || oocyte || female germline cell || presumptive oocyte
Cofilin-like	0.283	INHERITED FROM: border follicle cell
ZZ domain	0.283	INHERITED FROM: skeletal muscle of mesothorax || adult somatic muscle || indirect flight muscle || flight muscle || skeletal muscle of thorax
SMAD domain	0.283	INHERITED FROM: germline stem cell || female germline stem cell
EGF-type module	0.3345	INHERITED FROM: pigment cell || head mesoderm derived embryonic hemocyte || hub cell || embryonic precursor cell of adult midgut || dorsal acute muscle || somatic cell of testis || embryonic/larval midgut cell
Cap-Gly domain	0.3639	INHERITED FROM: interneuron
PDZ domain	0.3697	INHERITED FROM: somatic cell of ovary || epithelial cell
Motor proteins	0.3767	INHERITED FROM: germline cell
Cadherin	0.3862	INHERITED FROM: photoreceptor cell R4 || outer photoreceptor cell
G proteins	0.3982	INHERITED FROM: hemocyte
Homeodomain	0.4631	INHERITED FROM: uniglomerular antennal lobe projection neuron || thoracic neuroblast || glial cell || embryonic neuroblast || adult antennal lobe projection neuron VM2 adPN || adult antennal lobe projection neuron VA1v adPN || interneuron || dorsal margin photoreceptor || hypodermal muscle of prothorax || embryonic/larval neuron || U neuron || prothoracic ventral intersegmental muscle || ventral intersegmental muscle || maxillary palp olfactory receptor neuron || syncytium || muscle cell
Caspase catalytic domain	0.4632	INHERITED FROM: interommatidial precursor cell || peptidergic neuron || male germline cell
Fibronectin type III	0.4834	INHERITED FROM: embryonic heart cardioblast || prothoracic leg taste bristle chemosensory neuron || dendritic arborizing neuron || LNv neuron || abdominal neuron || adult pacemaker neuron || LN period neuron || s-LNv neuron || pacemaker neuron || gustatory receptor neuron || embryonic cardioblast || thoracic T1 neuron
Paired domain	0.5216	INHERITED FROM: EG neuron || EL neuron || RP2 motor neuron || U neuron
Cyclin	0.5216	INHERITED FROM: female germline cell
HLH, helix-loop-helix DNA-binding domain	0.5804	INHERITED FROM: EL neuron || 5-6I of thorax || sensory mother cell
Nuclear receptor ligand-binding domain	0.5939	INHERITED FROM: adult MBp lineage neuron || mushroom body intrinsic neuron || supraesophageal ganglion neuron || interneuron
Nuclear receptor	0.6189	INHERITED FROM: adult MBp lineage neuron || mushroom body intrinsic neuron || supraesophageal ganglion neuron || interneuron
Cytochrome P450	0.6991	INHERITED FROM: midline glial cell || neuropil associated CNS glial cell || CNS glial cell || embryonic/larval glial cell
Growth factor receptor domain	0.7679	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte
SH2 domain	0.7957	INHERITED FROM: photoreceptor cell || histaminergic neuron || photoreceptor cell R7 || rhabdomeric photoreceptor cell || cyst progenitor cell || sensory organ cell || optic lobe neuron
Forkhead DNA-binding domain	0.8337	INHERITED FROM: RP2sib neuron
FYVE, a phosphatidylinositol-3-phosphate binding domain	0.8355	INHERITED FROM: nephrocyte || embryonic/larval garland cell || garland cell
Hairy Orange domain	0.8355	INHERITED FROM: EG neuron || EL neuron
Classic zinc finger, C2H2	1	INHERITED FROM: embryonic ganglion mother cell

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)
PapD-like	0	DIRECT
Cullin repeat-like	0	DIRECT
YWTD domain	0	DIRECT
WWE domain	0	DIRECT
TIMP-like	0	DIRECT
Acetyl-CoA synthetase-like	0	DIRECT
NAD kinase/diacylglycerol kinase-like	0	DIRECT
Ferritin-like	0	DIRECT
Rhodanese/Cell cycle control phosphatase	0	DIRECT
PriA/YqbF domain	0	DIRECT
post-AAA+ oligomerization domain-like	0	DIRECT
Snake toxin-like	0	DIRECT
GINS helical bundle-like	0	DIRECT
Metal cation-transporting ATPase, ATP-binding domain N	0	DIRECT
Prefoldin	0	DIRECT
SAP domain	0	DIRECT
Ribosomal protein S5 domain 2-like	0	DIRECT
Mob1/phocein	0	DIRECT
Tropomyosin	0	DIRECT
Aminoacid dehydrogenase-like, N-terminal domain	0	DIRECT
ADC-like	0	DIRECT
Cullin homology domain	0	DIRECT
Translation proteins	0	DIRECT
Sema domain	0	DIRECT
B-box zinc-binding domain	0	DIRECT
NHL repeat	0	DIRECT
Class II aaRS ABD-related	0	DIRECT
Arginase/deacetylase	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
RNase III domain-like	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
SMAD MH1 domain	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Integrin alpha N-terminal domain	0	DIRECT
Plexin repeat	0	DIRECT
Metallo-hydrolase/oxidoreductase	0	DIRECT
Tubulin nucleotide-binding domain-like	0	DIRECT
Terpenoid synthases	0	DIRECT
alpha-catenin/vinculin-like	0	DIRECT
t-snare proteins	0	DIRECT
Integrin domains	0	DIRECT
CAD & PB1 domains	0	DIRECT
Smc hinge domain	0	DIRECT
RCC1/BLIP-II	0	DIRECT
Frizzled cysteine-rich domain	0	DIRECT
YVTN repeat-like/Quinoprotein amine dehydrogenase	0	DIRECT
MIR domain	0	DIRECT
Cytokine	0	DIRECT
Tubulin C-terminal domain-like	0	DIRECT
Concanavalin A-like lectins/glucanases	0.0009491	DIRECT
RING/U-box	0.02367	INHERITED FROM: embryonic/larval garland cell || garland cell
dsRNA-binding domain-like	0.04341	INHERITED FROM: alpha/beta Kenyon cell || Kenyon cell || antennal lobe projection neuron iPN || mushroom body intrinsic neuron || mushroom body extrinsic neuron || cholinergic neuron || antennal lobe projection neuron adPN || BAmv3 lineage neuron || unilateral ACT relay interneuron || uniglomerular antennal lobe projection neuron || persistent antennal lobe projection neuron || female germline stem cell
EGF/Laminin	0.05447	INHERITED FROM: ventral longitudinal muscle || abdominal 7 acute muscle || embryonic/larval midgut cell || somatic cell of testis || abdominal 6 acute muscle || abdominal 3 acute muscle || hub cell || pigment cell || eye photoreceptor cell stalk || tendon cell || sensory organ cell || embryonic precursor cell of adult midgut || pericardial cell || head mesoderm derived embryonic hemocyte || syncytium || sensory neuron || embryonic/larval somatic muscle || abdominal 2 acute muscle || glial cell || abdominal 5 acute muscle || nephrocyte || abdominal 4 acute muscle
p53-like transcription factors	0.06984	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte
Ankyrin repeat	0.07541	INHERITED FROM: Johnston organ neuron
Spectrin repeat	0.09674	INHERITED FROM: copper cell || enterocyte || oocyte || midgut enterocyte
Calponin-homology domain, CH-domain	0.1081	INHERITED FROM: flight muscle || indirect flight muscle || somatic muscle || skeletal muscle of thorax || skeletal muscle of mesothorax
Protein kinase-like (PK-like)	0.1337	INHERITED FROM: epithelial cell || photoreceptor cell R8 of pale ommatidium || intestinal stem cell
BAR/IMD domain-like	0.1344	INHERITED FROM: bouton || NMJ bouton || synapse
Homeodomain-like	0.1595	INHERITED FROM: U neuron || dorsal margin photoreceptor || embryonic neuroblast || adult antennal lobe projection neuron VA3 adPN || interneuron || adult antennal lobe projection neuron VM2 adPN || adult antennal lobe projection neuron VA1v adPN || prothoracic ventral intersegmental muscle || uniglomerular antennal lobe projection neuron || syncytium || muscle cell || embryonic/larval neuron || thoracic neuroblast
Actin depolymerizing proteins	0.1626	INHERITED FROM: follicle cell
Immunoglobulin	0.1743	INHERITED FROM: LNv neuron || 3-1M || embryonic heart cardioblast || embryonic cardioblast || adult pacemaker neuron || thoracic T1 neuron || pacemaker neuron || prothoracic leg taste bristle chemosensory neuron || longitudinal muscle || glial cell || LN period neuron || cardioblast
E set domains	0.2007	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte
Transducin (alpha subunit), insertion domain	0.2104	INHERITED FROM: eo neuron
PAZ domain	0.2738	INHERITED FROM: pole cell
CoA-dependent acyltransferases	0.2738	INHERITED FROM: flight muscle || adult somatic muscle || skeletal muscle of thorax || skeletal muscle of mesothorax
SAM/Pointed domain	0.3017	INHERITED FROM: muscle founder cell
Cadherin-like	0.3056	INHERITED FROM: photoreceptor cell R4
L domain-like	0.3469	INHERITED FROM: BAlc1 lineage neuron
Cap-Gly domain	0.3551	INHERITED FROM: interneuron
Metalloproteases ("zincins"), catalytic domain	0.4322	INHERITED FROM: embryonic heart cardioblast || embryonic cardioblast
Fibronectin type III	0.4441	INHERITED FROM: LNv neuron || s-LNv neuron || embryonic heart cardioblast || embryonic cardioblast || abdominal neuron || adult pacemaker neuron || dendritic arborizing neuron || thoracic T1 neuron || pacemaker neuron || prothoracic leg taste bristle chemosensory neuron || LN period neuron
Caspase-like	0.4504	INHERITED FROM: peptidergic neuron || interommatidial precursor cell || male germline cell
ENTH/VHS domain	0.4504	INHERITED FROM: imaginal disc epithelial cell
SMAD/FHA domain	0.5049	INHERITED FROM: female germline stem cell
FYVE/PHD zinc finger	0.526	INHERITED FROM: embryonic/larval garland cell
HLH, helix-loop-helix DNA-binding domain	0.536	INHERITED FROM: sensory mother cell || 5-6I of thorax || EL neuron
HAD-like	0.5409	INHERITED FROM: rhabdomere || rhabdomere of eye photoreceptor cell
Nuclear receptor ligand-binding domain	0.5698	INHERITED FROM: supraesophageal ganglion neuron || mushroom body intrinsic neuron || interneuron || adult MBp lineage neuron
Cytochrome P450	0.6813	INHERITED FROM: neuropil associated CNS glial cell || midline glial cell || embryonic/larval glial cell || CNS glial cell
Cyclin-like	0.6939	INHERITED FROM: female germline cell
Orange domain-like	0.7527	INHERITED FROM: 5-6I of thorax || EG neuron || EL neuron || thoracic neuron
Growth factor receptor domain	0.7619	INHERITED FROM: retinal pigment cell || somatic cell of testis || vMP2 neuron || hub cell || neuroblast NB5-2 || pigment cell || dMP2 neuron || embryonic cardioblast || surface associated glial cell || neuroblast of ventral nerve cord primordium || stage 1 neuroblast || dorsal acute muscle || photoreceptor cell R7 || GABAergic neuron || head mesoderm derived embryonic hemocyte || RP2sib neuron || acute muscle || cardioblast || embryonic hemocyte
SH2 domain	0.7717	INHERITED FROM: sensory organ cell || cyst progenitor cell || photoreceptor cell R7 || histaminergic neuron || photoreceptor cell || optic lobe neuron || rhabdomeric photoreceptor cell
Tetraspanin	0.8242	INHERITED FROM: sensory mother cell
beta-beta-alpha zinc fingers	1	INHERITED FROM: serotonergic neuron || subesophageal ganglion neuron || embryonic ganglion mother cell

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)
52490,55307 52490 - Tubulin nucleotide-binding domain-like 55307 - Tubulin C-terminal domain-like	0	DIRECT
74788,75632 74788 - Cullin repeat-like 75632 - Cullin homology domain	0	DIRECT
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat	0	DIRECT
57850,57850 57850 - RING/U-box 57850 - RING/U-box	0	DIRECT
75632,46785 75632 - Cullin homology domain 46785 - "Winged helix" DNA-binding domain	0	DIRECT
81660,56784 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like	0	DIRECT
47220,47220 47220 - alpha-catenin/vinculin-like 47220 - alpha-catenin/vinculin-like	0	DIRECT
52540,48019 52540 - P-loop containing nucleoside triphosphate hydrolases 48019 - post-AAA+ oligomerization domain-like	0	DIRECT
81296,81296 81296 - E set domains 81296 - E set domains	0	DIRECT
54768,54768 54768 - dsRNA-binding domain-like 54768 - dsRNA-binding domain-like	0	DIRECT
101912,103575 101912 - Sema domain 103575 - Plexin repeat	0	DIRECT
69318,69179 69318 - Integrin alpha N-terminal domain 69179 - Integrin domains	0	DIRECT
55753,55753 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins	0	DIRECT
49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
50692,54585 50692 - ADC-like 54585 - Cdc48 domain 2-like	0	DIRECT
69179,69179 69179 - Integrin domains 69179 - Integrin domains	0	DIRECT
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like	0	DIRECT
57903,47370 57903 - FYVE/PHD zinc finger 47370 - Bromodomain	0	DIRECT
49899,57196 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin	0	DIRECT
51206,51206 51206 - cAMP-binding domain-like 51206 - cAMP-binding domain-like	0	DIRECT
48403,48403 48403 - Ankyrin repeat 48403 - Ankyrin repeat	0	DIRECT
52777,52777 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases	0	DIRECT
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain)	0	DIRECT
63748,63748 63748 - Tudor/PWWP/MBT 63748 - Tudor/PWWP/MBT	0	DIRECT
57196,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
53223,51735 53223 - Aminoacid dehydrogenase-like, N-terminal domain 51735 - NAD(P)-binding Rossmann-fold domains	0	DIRECT
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin	0.08797	INHERITED FROM: LNv neuron || s-LNv neuron || embryonic/larval garland cell || embryonic heart cardioblast || embryonic cardioblast || adult pacemaker neuron || thoracic T1 neuron || interommatidial precursor cell || pacemaker neuron || prothoracic leg taste bristle chemosensory neuron || longitudinal muscle || cardioblast
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.1547	INHERITED FROM: somatic cell of testis || hub cell || eye photoreceptor cell stalk || secondary pigment cell || embryonic/larval pericardial cell || pericardial cell || histaminergic neuron || optic lobe neuron || embryonic/larval somatic muscle || nephrocyte || tertiary pigment cell || rhabdomeric photoreceptor cell
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.2104	INHERITED FROM: eo neuron
55550,50044 55550 - SH2 domain 50044 - SH3-domain	0.3551	INHERITED FROM: inner photoreceptor cell || photoreceptor cell R7
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like	0.3717	INHERITED FROM: outer photoreceptor cell || photoreceptor cell R4
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.4504	INHERITED FROM: abdominal sensory neuron || abdominal neuron || dendritic arborizing neuron || multidendritic neuron
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III	0.4527	INHERITED FROM: gustatory receptor neuron || LNv neuron || s-LNv neuron || embryonic heart cardioblast || neuropil associated CNS glial cell || embryonic cardioblast || chemosensory neuron || somatic muscle || adult pacemaker neuron || thoracic T1 neuron || giant fiber neuron || pacemaker neuron || prothoracic leg taste bristle chemosensory neuron || syncytium || longitudinal muscle || chemosensory system neuron || mechanosensory neuron || mechanosensory system neuron
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.6813	INHERITED FROM: female germline cell
47473,47473 47473 - EF-hand 47473 - EF-hand	0.7507	INHERITED FROM: bouton || synapse
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like	0.7527	INHERITED FROM: 5-6I of thorax || EG neuron || EL neuron || thoracic neuron
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.8371	INHERITED FROM: inner photoreceptor cell || somatic cell of testis || crystal cell || hub cell || pigment cell || photoreceptor cell R7 || head mesoderm derived embryonic hemocyte || embryonic hemocyte
57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	1	INHERITED FROM: embryonic ganglion mother cell

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)
74788,75632,46785 74788 - Cullin repeat-like 75632 - Cullin homology domain 46785 - "Winged helix" DNA-binding domain	0	DIRECT
48452,48452,48452 48452 - TPR-like 48452 - TPR-like 48452 - TPR-like	0	DIRECT
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat	0	DIRECT
57196,49899,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
57850,57850,57850 57850 - RING/U-box 57850 - RING/U-box 57850 - RING/U-box	0	DIRECT
49899,49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
69318,69179,69179 69318 - Integrin alpha N-terminal domain 69179 - Integrin domains 69179 - Integrin domains	0	DIRECT
81660,56784,81665 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like 81665 - Calcium ATPase, transmembrane domain M	0	DIRECT
57716,57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain)	0	DIRECT
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains	0	DIRECT
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin	0.04341	INHERITED FROM: somatic cell of testis || hub cell || eye photoreceptor cell stalk || photoreceptor cell R6 || photoreceptor cell R1 || sensory organ cell || secondary pigment cell || embryonic/larval pericardial cell || pericardial cell || head mesoderm derived embryonic hemocyte || histaminergic neuron || optic lobe neuron || embryonic/larval hypodermal muscle || sensory neuron || embryonic/larval somatic muscle || glial cell || nephrocyte || embryonic hemocyte || tertiary pigment cell || rhabdomeric photoreceptor cell
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III	0.2226	INHERITED FROM: gustatory receptor neuron || LNv neuron || s-LNv neuron || embryonic heart cardioblast || neuropil associated CNS glial cell || embryonic cardioblast || chemosensory neuron || adult pacemaker neuron || thoracic T1 neuron || giant fiber neuron || pacemaker neuron || prothoracic leg taste bristle chemosensory neuron || chemosensory system neuron || mechanosensory neuron || mechanosensory system neuron
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.2627	INHERITED FROM: gustatory receptor neuron || LNv neuron || s-LNv neuron || embryonic/larval garland cell || embryonic heart cardioblast || embryonic cardioblast || adult pacemaker neuron || thoracic T1 neuron || interommatidial precursor cell || pacemaker neuron || prothoracic leg taste bristle chemosensory neuron || mechanosensory neuron || mechanosensory system neuron
52540,52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0.3551	INHERITED FROM: male germline cell
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like	0.3717	INHERITED FROM: outer photoreceptor cell || photoreceptor cell R4
57667,57667,57667 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers 57667 - beta-beta-alpha zinc fingers	1	INHERITED FROM: embryonic ganglion mother cell

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.