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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)
post-AAA+ oligomerization domain-like	0	DIRECT
Integrin domains	0	DIRECT
Tropomyosin	0	DIRECT
Tubulin nucleotide-binding domain-like	0	DIRECT
Frizzled cysteine-rich domain	0	DIRECT
NAD kinase/diacylglycerol kinase-like	0	DIRECT
alpha-catenin/vinculin-like	0	DIRECT
Sema domain	0	DIRECT
Aminoacid dehydrogenase-like, N-terminal domain	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
MIR domain	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Acetyl-CoA synthetase-like	0	DIRECT
Cullin repeat-like	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Arginase/deacetylase	0	DIRECT
Rhodanese/Cell cycle control phosphatase	0	DIRECT
Ribosomal protein S5 domain 2-like	0	DIRECT
NHL repeat	0	DIRECT
RNase III domain-like	0	DIRECT
SAP domain	0	DIRECT
SMAD MH1 domain	0	DIRECT
Metal cation-transporting ATPase, ATP-binding domain N	0	DIRECT
Plexin repeat	0	DIRECT
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	0	DIRECT
Translation proteins	0	DIRECT
GINS helical bundle-like	0	DIRECT
PriA/YqbF domain	0	DIRECT
YWTD domain	0	DIRECT
WWE domain	0	DIRECT
Cytokine	0	DIRECT
PapD-like	0	DIRECT
Prefoldin	0	DIRECT
Integrin alpha N-terminal domain	0	DIRECT
Ferritin-like	0	DIRECT
Cullin homology domain	0	DIRECT
Metallo-hydrolase/oxidoreductase	0	DIRECT
Class II aaRS ABD-related	0	DIRECT
t-snare proteins	0	DIRECT
Smc hinge domain	0	DIRECT
Tubulin C-terminal domain-like	0	DIRECT
TIMP-like	0	DIRECT
RCC1/BLIP-II	0	DIRECT
YVTN repeat-like/Quinoprotein amine dehydrogenase	0	DIRECT
CAD & PB1 domains	0	DIRECT
Terpenoid synthases	0	DIRECT
ADC-like	0	DIRECT
Mob1/phocein	0	DIRECT
B-box zinc-binding domain	0	DIRECT
Snake toxin-like	0	DIRECT
RING/U-box	0.0329	INHERITED FROM: garland cell || embryonic/larval garland cell
dsRNA-binding domain-like	0.05681	INHERITED FROM: persistent antennal lobe projection neuron || uniglomerular antennal lobe projection neuron || Kenyon cell || unilateral ACT relay interneuron || cholinergic neuron || alpha/beta Kenyon cell || antennal lobe projection neuron adPN || BAmv3 lineage neuron || mushroom body extrinsic neuron || antennal lobe projection neuron iPN || mushroom body intrinsic neuron
EGF/Laminin	0.07112	INHERITED FROM: ventral longitudinal muscle || embryonic/larval somatic muscle || pericardial cell || embryonic precursor cell of adult midgut || abdominal 2 acute muscle || tendon cell || abdominal 5 acute muscle || syncytium || abdominal 7 acute muscle || embryonic/larval midgut cell || pigment cell || eye photoreceptor cell stalk || abdominal 6 acute muscle || abdominal 3 acute muscle || nephrocyte || hub cell || abdominal 4 acute muscle
p53-like transcription factors	0.08838	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte
Ankyrin repeat	0.09675	INHERITED FROM: Johnston organ neuron
Spectrin repeat	0.1188	INHERITED FROM: enterocyte || midgut enterocyte || copper cell
Calponin-homology domain, CH-domain	0.1324	INHERITED FROM: skeletal muscle of thorax || flight muscle || indirect flight muscle || skeletal muscle of mesothorax
BAR/IMD domain-like	0.1625	INHERITED FROM: bouton || NMJ bouton || synapse
Protein kinase-like (PK-like)	0.1702	INHERITED FROM: epithelial cell || intestinal stem cell || photoreceptor cell R8 of pale ommatidium
Homeodomain-like	0.1971	INHERITED FROM: U neuron || thoracic neuroblast || syncytium || embryonic/larval neuron || uniglomerular antennal lobe projection neuron || adult antennal lobe projection neuron VA1v adPN || embryonic neuroblast || prothoracic ventral intersegmental muscle || adult antennal lobe projection neuron VM2 adPN || muscle cell || interneuron || dorsal margin photoreceptor
Immunoglobulin	0.2102	INHERITED FROM: cardioblast || glial cell || longitudinal muscle || LN period neuron || embryonic heart cardioblast || adult pacemaker neuron || LNv neuron || pacemaker neuron || thoracic T1 neuron || embryonic cardioblast || prothoracic leg taste bristle chemosensory neuron
E set domains	0.2369	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte
Transducin (alpha subunit), insertion domain	0.2441	INHERITED FROM: eo neuron
PAZ domain	0.3097	INHERITED FROM: pole cell
CoA-dependent acyltransferases	0.3097	INHERITED FROM: skeletal muscle of thorax || flight muscle || adult somatic muscle || skeletal muscle of mesothorax
SAM/Pointed domain	0.3425	INHERITED FROM: muscle founder cell
Cadherin-like	0.3435	INHERITED FROM: photoreceptor cell R4
L domain-like	0.3902	INHERITED FROM: BAlc1 lineage neuron
Cap-Gly domain	0.3926	INHERITED FROM: interneuron
Metalloproteases ("zincins"), catalytic domain	0.474	INHERITED FROM: embryonic heart cardioblast || embryonic cardioblast
Caspase-like	0.4883	INHERITED FROM: male germline cell || peptidergic neuron || interommatidial precursor cell
Fibronectin type III	0.4883	INHERITED FROM: dendritic arborizing neuron || s-LNv neuron || embryonic heart cardioblast || adult pacemaker neuron || LNv neuron || pacemaker neuron || thoracic T1 neuron || abdominal neuron || embryonic cardioblast || prothoracic leg taste bristle chemosensory neuron
ENTH/VHS domain	0.4883	INHERITED FROM: imaginal disc epithelial cell
SMAD/FHA domain	0.5427	INHERITED FROM: female germline stem cell
FYVE/PHD zinc finger	0.5678	INHERITED FROM: embryonic/larval garland cell
HAD-like	0.5792	INHERITED FROM: rhabdomere of eye photoreceptor cell
HLH, helix-loop-helix DNA-binding domain	0.5795	INHERITED FROM: sensory mother cell || 5-6I of thorax
Nuclear receptor ligand-binding domain	0.6081	INHERITED FROM: supraesophageal ganglion neuron || interneuron || adult MBp lineage neuron || mushroom body intrinsic neuron
Cytochrome P450	0.7124	INHERITED FROM: CNS glial cell || embryonic/larval glial cell || neuropil associated CNS glial cell || midline glial cell
Cyclin-like	0.7259	INHERITED FROM: female germline cell
Orange domain-like	0.7802	INHERITED FROM: EG neuron || 5-6I of thorax || EL neuron
Growth factor receptor domain	0.7903	INHERITED FROM: somatic cell of testis || head mesoderm derived embryonic hemocyte || embryonic hemocyte || GABAergic neuron || photoreceptor cell R7 || pigment cell || retinal pigment cell || stage 1 neuroblast || neuroblast NB5-2 || dorsal acute muscle || surface associated glial cell || RP2sib neuron || dMP2 neuron || hub cell || vMP2 neuron
SH2 domain	0.8006	INHERITED FROM: optic lobe neuron || sensory organ cell || photoreceptor cell || photoreceptor cell R7 || histaminergic neuron || cyst progenitor cell || rhabdomeric photoreceptor cell
Tetraspanin	0.8471	INHERITED FROM: sensory mother cell
beta-beta-alpha zinc fingers	1	INHERITED FROM: serotonergic neuron || subesophageal ganglion 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)
Choline/Carnitine O-acyltransferase	0	DIRECT
Smc hinge domain	0	DIRECT
BAR domain	0	DIRECT
SAP domain	0	DIRECT
MSP-like	0	DIRECT
2Fe-2S ferredoxin domains from multidomain proteins	0	DIRECT
YWTD domain	0	DIRECT
Acetyl-CoA synthetase-like	0	DIRECT
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	0	DIRECT
Tubulin, C-terminal domain	0	DIRECT
B-box zinc-binding domain	0	DIRECT
Extracellular domain of cell surface receptors	0	DIRECT
Tetramerization domain of potassium channels	0	DIRECT
Sema domain	0	DIRECT
Arrestin/Vps26-like	0	DIRECT
Isoprenyl diphosphate synthases	0	DIRECT
Zf-UBP	0	DIRECT
CAD domain	0	DIRECT
POU-specific domain	0	DIRECT
Aminoacid dehydrogenase-like, C-terminal domain	0	DIRECT
Plexin repeat	0	DIRECT
Anticodon-binding domain of Class II aaRS	0	DIRECT
RNase III catalytic domain-like	0	DIRECT
Group II chaperonin (CCT, TRIC), intermediate domain	0	DIRECT
Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta	0	DIRECT
Myb/SANT domain	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Frizzled cysteine-rich domain	0	DIRECT
DNA polymerase III clamp loader subunits, C-terminal domain	0	DIRECT
SPRY domain	0	DIRECT
Fibroblast growth factors (FGF)	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
Laminin-type module	0	DIRECT
Glutathione S-transferase (GST), N-terminal domain	0	DIRECT
WWE domain	0	DIRECT
Transforming growth factor (TGF)-beta	0	DIRECT
Cullin homology domain	0	DIRECT
Cell cycle control phosphatase, catalytic domain	0	DIRECT
t-snare proteins	0	DIRECT
Inositol polyphosphate 5-phosphatase (IPP5)	0	DIRECT
Metal cation-transporting ATPase, ATP-binding domain N	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Histone deacetylase, HDAC	0	DIRECT
Diacylglycerol kinase-like	0	DIRECT
Mob1/phocein	0	DIRECT
Tropomyosin	0	DIRECT
MIR domain	0	DIRECT
Nitrogenase iron protein-like	0	DIRECT
Cullin repeat	0	DIRECT
Proteasome subunits	0	DIRECT
Integrin alpha N-terminal domain	0	DIRECT
Armadillo repeat	0	DIRECT
beta-CASP RNA-metabolising hydrolases	0	DIRECT
SMAD MH1 domain	0	DIRECT
Laminin G-like module	0	DIRECT
NHL repeat	0	DIRECT
SCF ubiquitin ligase complex WHB domain	0	DIRECT
Eps15 homology domain (EH domain)	0	DIRECT
Extended AAA-ATPase domain	0	DIRECT
MBT repeat	0	DIRECT
Kelch motif	0	DIRECT
Prefoldin	0	DIRECT
Integrin domains	0	DIRECT
Tubulin, GTPase domain	0	DIRECT
Ankyrin repeat	0.09492	INHERITED FROM: ventral multidendritic neuron || Johnston organ neuron
Spectrin repeat	0.1058	INHERITED FROM: enterocyte || midgut enterocyte || copper cell || oocyte
Calponin-homology domain, CH-domain	0.1214	INHERITED FROM: skeletal muscle of thorax || flight muscle || indirect flight muscle || skeletal muscle of mesothorax
T-box	0.1735	INHERITED FROM: embryonic/larval hypodermal muscle
PLC-like (P variant)	0.1735	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte || dorsal multidendritic neuron ddaC || dorsal multidendritic neuron
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.1735	INHERITED FROM: intestinal stem cell
Transducin (alpha subunit), insertion domain	0.2217	INHERITED FROM: eo neuron
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0.2217	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte || lamellocyte
Protein kinases, catalytic subunit	0.2392	INHERITED FROM: intestinal stem cell || photoreceptor cell R8 of pale ommatidium
I set domains	0.256	INHERITED FROM: cardioblast || gustatory system neuron || dendritic arborizing neuron || abdominal sensory neuron || s-LNv neuron || interface glial cell || embryonic heart cardioblast || mechanosensory system neuron || adult pacemaker neuron || LNv neuron || pacemaker neuron || gustatory receptor neuron || thoracic T1 neuron || abdominal neuron || visceral muscle fiber || embryonic cardioblast || prothoracic leg taste bristle chemosensory neuron
RecA protein-like (ATPase-domain)	0.2853	INHERITED FROM: female germline cell || oocyte || nurse cell || presumptive oocyte
SMAD domain	0.2853	INHERITED FROM: germline stem cell || female germline stem cell
ZZ domain	0.2853	INHERITED FROM: skeletal muscle of thorax || flight muscle || indirect flight muscle || adult somatic muscle || skeletal muscle of mesothorax
Pancreatic lipase, N-terminal domain	0.2853	INHERITED FROM: ganglion mother cell
EGF-type module	0.3397	INHERITED FROM: somatic cell of testis || head mesoderm derived embryonic hemocyte || embryonic precursor cell of adult midgut || embryonic/larval midgut cell || pigment cell || dorsal acute muscle || hub cell
Cap-Gly domain	0.3667	INHERITED FROM: interneuron
PDZ domain	0.3773	INHERITED FROM: epithelial cell || somatic cell of ovary
Motor proteins	0.3836	INHERITED FROM: germline cell
Cadherin	0.3901	INHERITED FROM: photoreceptor cell R4 || outer photoreceptor cell
G proteins	0.4093	INHERITED FROM: hemocyte
Homeodomain	0.4786	INHERITED FROM: U neuron || hypodermal muscle of prothorax || thoracic neuroblast || glial cell || syncytium || ventral intersegmental muscle || embryonic/larval neuron || uniglomerular antennal lobe projection neuron || adult antennal lobe projection neuron VA1v adPN || embryonic neuroblast || prothoracic ventral intersegmental muscle || adult antennal lobe projection neuron VM2 adPN || muscle cell || interneuron || dorsal margin photoreceptor || maxillary palp olfactory receptor neuron
Fibronectin type III	0.494	INHERITED FROM: dendritic arborizing neuron || s-LNv neuron || LN period neuron || embryonic heart cardioblast || adult pacemaker neuron || LNv neuron || pacemaker neuron || gustatory receptor neuron || thoracic T1 neuron || abdominal neuron || embryonic cardioblast || prothoracic leg taste bristle chemosensory neuron
Paired domain	0.5271	INHERITED FROM: U neuron || RP2 motor neuron || EG neuron || EL neuron
Cyclin	0.5271	INHERITED FROM: female germline cell
Caspase catalytic domain	0.5574	INHERITED FROM: peptidergic neuron
HLH, helix-loop-helix DNA-binding domain	0.5918	INHERITED FROM: sensory mother cell || 5-6I of thorax || EL neuron
Nuclear receptor ligand-binding domain	0.6005	INHERITED FROM: supraesophageal ganglion neuron || interneuron || adult MBp lineage neuron || mushroom body intrinsic neuron
Nuclear receptor	0.6264	INHERITED FROM: supraesophageal ganglion neuron || interneuron || adult MBp lineage neuron || mushroom body intrinsic neuron
Cytochrome P450	0.7046	INHERITED FROM: CNS glial cell || embryonic/larval glial cell || neuropil associated CNS glial cell || midline glial cell
Growth factor receptor domain	0.7731	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte
SH2 domain	0.8019	INHERITED FROM: optic lobe neuron || sensory organ cell || photoreceptor cell || photoreceptor cell R7 || histaminergic neuron || cyst progenitor cell || rhabdomeric photoreceptor cell
Forkhead DNA-binding domain	0.8375	INHERITED FROM: RP2sib neuron
Hairy Orange domain	0.8397	INHERITED FROM: EG neuron || EL neuron
FYVE, a phosphatidylinositol-3-phosphate binding domain	0.8397	INHERITED FROM: nephrocyte || garland cell || embryonic/larval garland cell
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)
Tropomyosin	0	DIRECT
MIR domain	0	DIRECT
Translation proteins	0	DIRECT
post-AAA+ oligomerization domain-like	0	DIRECT
Smc hinge domain	0	DIRECT
Prefoldin	0	DIRECT
Metal cation-transporting ATPase, ATP-binding domain N	0	DIRECT
SMAD MH1 domain	0	DIRECT
Tubulin C-terminal domain-like	0	DIRECT
Metallo-hydrolase/oxidoreductase	0	DIRECT
Plexin repeat	0	DIRECT
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	0	DIRECT
Ribosomal protein S5 domain 2-like	0	DIRECT
Cdc48 domain 2-like	0	DIRECT
ADC-like	0	DIRECT
Tubulin nucleotide-binding domain-like	0	DIRECT
NHL repeat	0	DIRECT
Terpenoid synthases	0	DIRECT
Arginase/deacetylase	0	DIRECT
Frizzled cysteine-rich domain	0	DIRECT
B-box zinc-binding domain	0	DIRECT
Aminoacid dehydrogenase-like, N-terminal domain	0	DIRECT
Class II aaRS ABD-related	0	DIRECT
GINS helical bundle-like	0	DIRECT
t-snare proteins	0	DIRECT
RCC1/BLIP-II	0	DIRECT
Acetyl-CoA synthetase-like	0	DIRECT
WWE domain	0	DIRECT
PapD-like	0	DIRECT
YWTD domain	0	DIRECT
Ferritin-like	0	DIRECT
Integrin alpha N-terminal domain	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
RNase III domain-like	0	DIRECT
Snake toxin-like	0	DIRECT
Cullin homology domain	0	DIRECT
TIMP-like	0	DIRECT
Cullin repeat-like	0	DIRECT
alpha-catenin/vinculin-like	0	DIRECT
PriA/YqbF domain	0	DIRECT
Integrin domains	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Sema domain	0	DIRECT
Cytokine	0	DIRECT
NAD kinase/diacylglycerol kinase-like	0	DIRECT
Mob1/phocein	0	DIRECT
CAD & PB1 domains	0	DIRECT
YVTN repeat-like/Quinoprotein amine dehydrogenase	0	DIRECT
Rhodanese/Cell cycle control phosphatase	0	DIRECT
SAP domain	0	DIRECT
RING/U-box	0.0253	INHERITED FROM: embryonic/larval garland cell || garland cell
dsRNA-binding domain-like	0.04482	INHERITED FROM: unilateral ACT relay interneuron || alpha/beta Kenyon cell || antennal lobe projection neuron iPN || persistent antennal lobe projection neuron || Kenyon cell || uniglomerular antennal lobe projection neuron || mushroom body extrinsic neuron || cholinergic neuron || antennal lobe projection neuron adPN || mushroom body intrinsic neuron || BAmv3 lineage neuron || female germline stem cell
EGF/Laminin	0.0571	INHERITED FROM: abdominal 3 acute muscle || nephrocyte || hub cell || glial cell || embryonic precursor cell of adult midgut || eye photoreceptor cell stalk || tendon cell || embryonic/larval midgut cell || ventral longitudinal muscle || sensory organ cell || somatic cell of testis || abdominal 5 acute muscle || abdominal 2 acute muscle || abdominal 4 acute muscle || embryonic/larval somatic muscle || abdominal 6 acute muscle || syncytium || sensory neuron || abdominal 7 acute muscle || pericardial cell || pigment cell
p53-like transcription factors	0.07209	INHERITED FROM: embryonic hemocyte || head mesoderm derived embryonic hemocyte
Ankyrin repeat	0.07916	INHERITED FROM: Johnston organ neuron
Spectrin repeat	0.0987	INHERITED FROM: enterocyte || oocyte || midgut enterocyte || copper cell
Calponin-homology domain, CH-domain	0.1109	INHERITED FROM: skeletal muscle of mesothorax || skeletal muscle of thorax || flight muscle || somatic muscle || indirect flight muscle
BAR/IMD domain-like	0.1379	INHERITED FROM: NMJ bouton || bouton || synapse
Protein kinase-like (PK-like)	0.1451	INHERITED FROM: epithelial cell || photoreceptor cell R8 of pale ommatidium || intestinal stem cell
Actin depolymerizing proteins	0.1652	INHERITED FROM: follicle cell
Homeodomain-like	0.1698	INHERITED FROM: prothoracic ventral intersegmental muscle || U neuron || adult antennal lobe projection neuron VM2 adPN || embryonic neuroblast || adult antennal lobe projection neuron VA1v adPN || embryonic/larval neuron || uniglomerular antennal lobe projection neuron || thoracic neuroblast || interneuron || dorsal margin photoreceptor || muscle cell || syncytium || adult antennal lobe projection neuron VA3 adPN
Immunoglobulin	0.1819	INHERITED FROM: embryonic heart cardioblast || adult pacemaker neuron || pacemaker neuron || cardioblast || glial cell || LN period neuron || prothoracic leg taste bristle chemosensory neuron || LNv neuron || thoracic T1 neuron || longitudinal muscle || embryonic cardioblast
E set domains	0.2068	INHERITED FROM: embryonic hemocyte || head mesoderm derived embryonic hemocyte
Transducin (alpha subunit), insertion domain	0.2138	INHERITED FROM: eo neuron
PAZ domain	0.2769	INHERITED FROM: pole cell
CoA-dependent acyltransferases	0.2769	INHERITED FROM: skeletal muscle of mesothorax || skeletal muscle of thorax || flight muscle || adult somatic muscle
SAM/Pointed domain	0.3088	INHERITED FROM: muscle founder cell
Cadherin-like	0.3097	INHERITED FROM: photoreceptor cell R4
L domain-like	0.3563	INHERITED FROM: BAlc1 lineage neuron
Cap-Gly domain	0.3584	INHERITED FROM: interneuron
Metalloproteases ("zincins"), catalytic domain	0.4405	INHERITED FROM: embryonic heart cardioblast || embryonic cardioblast
Fibronectin type III	0.4551	INHERITED FROM: embryonic heart cardioblast || adult pacemaker neuron || pacemaker neuron || dendritic arborizing neuron || LN period neuron || prothoracic leg taste bristle chemosensory neuron || LNv neuron || abdominal neuron || thoracic T1 neuron || s-LNv neuron || embryonic cardioblast
Caspase-like	0.4551	INHERITED FROM: interommatidial precursor cell || male germline cell || peptidergic neuron
ENTH/VHS domain	0.4551	INHERITED FROM: imaginal disc epithelial cell
SMAD/FHA domain	0.5105	INHERITED FROM: female germline stem cell
FYVE/PHD zinc finger	0.5365	INHERITED FROM: embryonic/larval garland cell
HAD-like	0.5478	INHERITED FROM: rhabdomere of eye photoreceptor cell || rhabdomere
HLH, helix-loop-helix DNA-binding domain	0.5481	INHERITED FROM: EL neuron || sensory mother cell || 5-6I of thorax
Nuclear receptor ligand-binding domain	0.5775	INHERITED FROM: adult MBp lineage neuron || interneuron || mushroom body intrinsic neuron || supraesophageal ganglion neuron
Cytochrome P450	0.6869	INHERITED FROM: midline glial cell || CNS glial cell || neuropil associated CNS glial cell || embryonic/larval glial cell
Cyclin-like	0.7007	INHERITED FROM: female germline cell
Orange domain-like	0.7579	INHERITED FROM: thoracic neuron || EL neuron || 5-6I of thorax || EG neuron
Growth factor receptor domain	0.7682	INHERITED FROM: RP2sib neuron || embryonic hemocyte || dorsal acute muscle || cardioblast || hub cell || head mesoderm derived embryonic hemocyte || surface associated glial cell || photoreceptor cell R7 || somatic cell of testis || dMP2 neuron || neuroblast NB5-2 || vMP2 neuron || retinal pigment cell || stage 1 neuroblast || neuroblast of ventral nerve cord primordium || acute muscle || GABAergic neuron || pigment cell || embryonic cardioblast
SH2 domain	0.7791	INHERITED FROM: histaminergic neuron || sensory organ cell || photoreceptor cell R7 || optic lobe neuron || photoreceptor cell || cyst progenitor cell || rhabdomeric photoreceptor cell
Tetraspanin	0.8285	INHERITED FROM: sensory mother cell
beta-beta-alpha zinc fingers	1	INHERITED FROM: embryonic ganglion mother cell || subesophageal ganglion neuron || serotonergic neuron

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)
69179,69179 69179 - Integrin domains 69179 - Integrin domains	0	DIRECT
52540,48019 52540 - P-loop containing nucleoside triphosphate hydrolases 48019 - post-AAA+ oligomerization domain-like	0	DIRECT
53223,51735 53223 - Aminoacid dehydrogenase-like, N-terminal domain 51735 - NAD(P)-binding Rossmann-fold domains	0	DIRECT
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
101912,103575 101912 - Sema domain 103575 - Plexin repeat	0	DIRECT
48403,48403 48403 - Ankyrin repeat 48403 - Ankyrin repeat	0	DIRECT
49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain)	0	DIRECT
81660,56784 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like	0	DIRECT
51206,51206 51206 - cAMP-binding domain-like 51206 - cAMP-binding domain-like	0	DIRECT
55753,55753 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins	0	DIRECT
81296,81296 81296 - E set domains 81296 - E set domains	0	DIRECT
47220,47220 47220 - alpha-catenin/vinculin-like 47220 - alpha-catenin/vinculin-like	0	DIRECT
57850,57850 57850 - RING/U-box 57850 - RING/U-box	0	DIRECT
52777,52777 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases	0	DIRECT
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like	0	DIRECT
63748,63748 63748 - Tudor/PWWP/MBT 63748 - Tudor/PWWP/MBT	0	DIRECT
54768,54768 54768 - dsRNA-binding domain-like 54768 - dsRNA-binding domain-like	0	DIRECT
57903,47370 57903 - FYVE/PHD zinc finger 47370 - Bromodomain	0	DIRECT
75632,46785 75632 - Cullin homology domain 46785 - "Winged helix" DNA-binding domain	0	DIRECT
50692,54585 50692 - ADC-like 54585 - Cdc48 domain 2-like	0	DIRECT
69318,69179 69318 - Integrin alpha N-terminal domain 69179 - Integrin domains	0	DIRECT
57196,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat	0	DIRECT
49899,57196 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin	0	DIRECT
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin	0.09236	INHERITED FROM: embryonic heart cardioblast || adult pacemaker neuron || pacemaker neuron || cardioblast || interommatidial precursor cell || embryonic/larval garland cell || prothoracic leg taste bristle chemosensory neuron || LNv neuron || thoracic T1 neuron || s-LNv neuron || longitudinal muscle || embryonic cardioblast
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.1587	INHERITED FROM: nephrocyte || histaminergic neuron || hub cell || eye photoreceptor cell stalk || secondary pigment cell || embryonic/larval pericardial cell || tertiary pigment cell || somatic cell of testis || optic lobe neuron || embryonic/larval somatic muscle || pericardial cell || rhabdomeric photoreceptor cell
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.2138	INHERITED FROM: eo neuron
55550,50044 55550 - SH2 domain 50044 - SH3-domain	0.3584	INHERITED FROM: photoreceptor cell R7 || inner photoreceptor cell
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like	0.3768	INHERITED FROM: photoreceptor cell R4 || outer photoreceptor cell
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.4551	INHERITED FROM: dendritic arborizing neuron || multidendritic neuron || abdominal neuron || abdominal sensory neuron
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III	0.46	INHERITED FROM: embryonic heart cardioblast || adult pacemaker neuron || pacemaker neuron || gustatory receptor neuron || mechanosensory neuron || giant fiber neuron || chemosensory system neuron || prothoracic leg taste bristle chemosensory neuron || neuropil associated CNS glial cell || mechanosensory system neuron || LNv neuron || thoracic T1 neuron || s-LNv neuron || somatic muscle || syncytium || chemosensory neuron || longitudinal muscle || embryonic cardioblast
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.6869	INHERITED FROM: female germline cell
47473,47473 47473 - EF-hand 47473 - EF-hand	0.7551	INHERITED FROM: bouton || synapse
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like	0.7579	INHERITED FROM: thoracic neuron || EL neuron || 5-6I of thorax || EG neuron
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.8405	INHERITED FROM: embryonic hemocyte || hub cell || head mesoderm derived embryonic hemocyte || photoreceptor cell R7 || somatic cell of testis || inner photoreceptor cell || crystal cell || pigment cell
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)
49899,49899,49899 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains	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
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat	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
69318,69179,69179 69318 - Integrin alpha N-terminal domain 69179 - Integrin domains 69179 - Integrin domains	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
48452,48452,48452 48452 - TPR-like 48452 - TPR-like 48452 - TPR-like	0	DIRECT
74788,75632,46785 74788 - Cullin repeat-like 75632 - Cullin homology domain 46785 - "Winged helix" DNA-binding domain	0	DIRECT
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin	0.04482	INHERITED FROM: nephrocyte || histaminergic neuron || embryonic hemocyte || hub cell || glial cell || head mesoderm derived embryonic hemocyte || eye photoreceptor cell stalk || photoreceptor cell R1 || secondary pigment cell || sensory organ cell || embryonic/larval pericardial cell || tertiary pigment cell || somatic cell of testis || embryonic/larval hypodermal muscle || photoreceptor cell R6 || optic lobe neuron || embryonic/larval somatic muscle || sensory neuron || pericardial cell || rhabdomeric photoreceptor cell
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III	0.2278	INHERITED FROM: embryonic heart cardioblast || adult pacemaker neuron || pacemaker neuron || gustatory receptor neuron || mechanosensory neuron || giant fiber neuron || chemosensory system neuron || prothoracic leg taste bristle chemosensory neuron || neuropil associated CNS glial cell || mechanosensory system neuron || LNv neuron || thoracic T1 neuron || s-LNv neuron || chemosensory neuron || embryonic cardioblast
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.2698	INHERITED FROM: embryonic heart cardioblast || adult pacemaker neuron || pacemaker neuron || gustatory receptor neuron || interommatidial precursor cell || mechanosensory neuron || embryonic/larval garland cell || prothoracic leg taste bristle chemosensory neuron || mechanosensory system neuron || LNv neuron || thoracic T1 neuron || s-LNv neuron || embryonic cardioblast
52540,52540,52540 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases 52540 - P-loop containing nucleoside triphosphate hydrolases	0.3584	INHERITED FROM: male germline cell
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like	0.3768	INHERITED FROM: photoreceptor cell R4 || outer photoreceptor cell
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.