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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 (SDFA level: Least Informative)
Highlighted in gray are those with FDR_all>0.001

SCOP term	FDR (all)	Annotation (direct or inherited)
B-box zinc-binding domain	0	DIRECT
Prefoldin	0	DIRECT
Smc hinge domain	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Rhodanese/Cell cycle control phosphatase	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
TIMP-like	0	DIRECT
PapD-like	0	DIRECT
NHL repeat	0	DIRECT
MIR domain	0	DIRECT
Cullin repeat-like	0	DIRECT
Tropomyosin	0	DIRECT
CAD & PB1 domains	0	DIRECT
GINS helical bundle-like	0	DIRECT
Mob1/phocein	0	DIRECT
Sema domain	0	DIRECT
Tubulin C-terminal domain-like	0	DIRECT
Frizzled cysteine-rich domain	0	DIRECT
t-snare proteins	0	DIRECT
Arginase/deacetylase	0	DIRECT
SMAD MH1 domain	0	DIRECT
Integrin domains	0	DIRECT
Plexin repeat	0	DIRECT
Aminoacid dehydrogenase-like, N-terminal domain	0	DIRECT
YVTN repeat-like/Quinoprotein amine dehydrogenase	0	DIRECT
SAP domain	0	DIRECT
Snake toxin-like	0	DIRECT
Ferritin-like	0	DIRECT
YWTD domain	0	DIRECT
Tubulin nucleotide-binding domain-like	0	DIRECT
Terpenoid synthases	0	DIRECT
NAD kinase/diacylglycerol kinase-like	0	DIRECT
PriA/YqbF domain	0	DIRECT
alpha-catenin/vinculin-like	0	DIRECT
Metallo-hydrolase/oxidoreductase	0	DIRECT
RNase III domain-like	0	DIRECT
Cullin homology domain	0	DIRECT
Metal cation-transporting ATPase, ATP-binding domain N	0	DIRECT
post-AAA+ oligomerization domain-like	0	DIRECT
Ribosomal protein S5 domain 2-like	0	DIRECT
Class II aaRS ABD-related	0	DIRECT
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	0	DIRECT
Cytokine	0	DIRECT
Ankyrin repeat	0.01209	INHERITED FROM: Johnston organ neuron
p53-like transcription factors	0.0168	INHERITED FROM: embryonic hemocyte || head mesoderm derived embryonic hemocyte
dsRNA-binding domain-like	0.03823	INHERITED FROM: mushroom body extrinsic neuron || cholinergic neuron || germline cell || antennal lobe projection neuron || adult MBp lineage neuron || adult uniglomerular antennal lobe projection neuron adPN || mushroom body intrinsic neuron || projection neuron || persistent antennal lobe projection neuron || alpha/beta Kenyon cell || unilateral ACT relay interneuron || BAmv3 lineage neuron || female germline stem cell || adult antennal lobe projection neuron || adult antennal lobe projection neuron adPN || antennal lobe projection neuron adPN || Kenyon cell || medial antennal lobe tract projection neuron || uniglomerular antennal lobe projection neuron || adult antennal lobe projection neuron DL1 adPN
Homeodomain-like	0.06019	INHERITED FROM: A1-7 ventral acute muscle 1 || EL neuron || dorsal margin photoreceptor || interneuron || thoracic neuroblast || U neuron || embryonic neuroblast || prothoracic ventral intersegmental muscle || embryonic/larval neuron || uniglomerular antennal lobe projection neuron
Protein kinase-like (PK-like)	0.06986	INHERITED FROM: somatic cell of ovariole || intestinal stem cell
EGF/Laminin	0.08661	INHERITED FROM: abdominal 5 dorsal acute muscle 1 || abdominal 3 dorsal acute muscle 1 || abdominal 7 dorsal acute muscle 1 || embryonic/larval midgut cell || abdominal 4 dorsal acute muscle 1 || tendon cell || sensory neuron || nephrocyte || adult midgut progenitor cell || glial cell || abdominal 2 dorsal acute muscle 1 || hub cell || eye photoreceptor cell stalk || ventral longitudinal muscle || somatic muscle || sensory organ cell || A1-7 ventral longitudinal muscle 1 || syncytium || pericardial cell || embryonic/larval somatic muscle || abdominal 6 dorsal acute muscle 1
E set domains	0.08863	INHERITED FROM: embryonic hemocyte || head mesoderm derived embryonic hemocyte
Spectrin repeat	0.1084	INHERITED FROM: fat cell || copper cell || oocyte || enterocyte
RING/U-box	0.1086	INHERITED FROM: garland cell || embryonic/larval garland cell
BAR/IMD domain-like	0.1463	INHERITED FROM: NMJ bouton || bouton || synapse
Actin depolymerizing proteins	0.1796	INHERITED FROM: follicle cell
Transducin (alpha subunit), insertion domain	0.2307	INHERITED FROM: eo neuron
L domain-like	0.2316	INHERITED FROM: BAlc1 lineage neuron
Calponin-homology domain, CH-domain	0.2354	INHERITED FROM: indirect flight muscle || flight muscle
Immunoglobulin	0.25	INHERITED FROM: pacemaker neuron || LN period neuron || longitudinal muscle || cardioblast || LNv neuron || leg taste bristle chemosensory neuron || embryonic cardioblast || embryonic heart cardioblast || adult pacemaker neuron
PAZ domain	0.2961	INHERITED FROM: pole cell
Cadherin-like	0.3236	INHERITED FROM: photoreceptor cell R4
Fibronectin type III	0.3683	INHERITED FROM: pacemaker neuron || LN period neuron || LNv neuron || leg taste bristle chemosensory neuron || s-LNv neuron || embryonic heart cardioblast || adult pacemaker neuron
Cap-Gly domain	0.3795	INHERITED FROM: interneuron
ENTH/VHS domain	0.4683	INHERITED FROM: imaginal disc epithelial cell
Caspase-like	0.4683	INHERITED FROM: peptidergic neuron || interommatidial precursor cell
HAD-like	0.4873	INHERITED FROM: rhabdomere of eye photoreceptor cell
Metalloproteases ("zincins"), catalytic domain	0.4885	INHERITED FROM: embryonic cardioblast || embryonic heart cardioblast
SMAD/FHA domain	0.5191	INHERITED FROM: female germline stem cell
HLH, helix-loop-helix DNA-binding domain	0.5269	INHERITED FROM: EL neuron || sensory mother cell
CoA-dependent acyltransferases	0.559	INHERITED FROM: skeletal muscle of mesothorax || flight muscle || skeletal muscle of thorax || adult somatic muscle
Nuclear receptor ligand-binding domain	0.5754	INHERITED FROM: supraesophageal ganglion neuron || mushroom body intrinsic neuron || interneuron
Cytochrome P450	0.6885	INHERITED FROM: neuropil associated CNS glial cell || CNS glial cell || midline glial cell || embryonic/larval glial cell || larval VNC neuropil glial cell || larval neuropil glial cell
Cyclin-like	0.6986	INHERITED FROM: female germline cell
Growth factor receptor domain	0.7074	INHERITED FROM: RP2sib neuron || stage 1 neuroblast || dMP2 neuron || photoreceptor cell R7 || surface associated glial cell || vMP2 neuron || embryonic hemocyte || head mesoderm derived embryonic hemocyte || GABAergic neuron || neuroblast NB5-2 || dorsal acute muscle || somatic cell of testis
Orange domain-like	0.7587	INHERITED FROM: EL neuron || EG neuron || 5-6I of thorax
Tetraspanin	0.8274	INHERITED FROM: sensory mother cell
SH2 domain	0.8525	INHERITED FROM: photoreceptor cell || rhabdomeric photoreceptor cell || histaminergic neuron || photoreceptor cell R7 || cyst progenitor cell || sensory organ cell || adult optic lobe neuron
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)
Myb/SANT domain	0	DIRECT
RNase III catalytic domain-like	0	DIRECT
Laminin G-like module	0	DIRECT
Isoprenyl diphosphate synthases	0	DIRECT
MSP-like	0	DIRECT
NHL repeat	0	DIRECT
Eps15 homology domain (EH domain)	0	DIRECT
Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta	0	DIRECT
CAD domain	0	DIRECT
Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	0	DIRECT
Rel/Dorsal transcription factors, DNA-binding domain	0	DIRECT
Kelch motif	0	DIRECT
Tubulin, C-terminal domain	0	DIRECT
CoA-binding domain	0	DIRECT
MBT repeat	0	DIRECT
Nitrogenase iron protein-like	0	DIRECT
Anticodon-binding domain of Class II aaRS	0	DIRECT
Tubulin, GTPase domain	0	DIRECT
DNA polymerase III clamp loader subunits, C-terminal domain	0	DIRECT
SCF ubiquitin ligase complex WHB domain	0	DIRECT
Fibroblast growth factors (FGF)	0	DIRECT
t-snare proteins	0	DIRECT
Metal cation-transporting ATPase, ATP-binding domain N	0	DIRECT
BAR domain	0	DIRECT
Frizzled cysteine-rich domain	0	DIRECT
Group II chaperonin (CCT, TRIC), intermediate domain	0	DIRECT
SMAD MH1 domain	0	DIRECT
Cullin homology domain	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
YWTD domain	0	DIRECT
SPRY domain	0	DIRECT
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	0	DIRECT
beta-CASP RNA-metabolising hydrolases	0	DIRECT
Tropomyosin	0	DIRECT
Aminoacid dehydrogenase-like, C-terminal domain	0	DIRECT
Diacylglycerol kinase-like	0	DIRECT
NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	0	DIRECT
Plexin repeat	0	DIRECT
Pointed domain	0	DIRECT
B-box zinc-binding domain	0	DIRECT
Inositol polyphosphate 5-phosphatase (IPP5)	0	DIRECT
Extracellular domain of cell surface receptors	0	DIRECT
Histone deacetylase, HDAC	0	DIRECT
Transforming growth factor (TGF)-beta	0	DIRECT
Sema domain	0	DIRECT
Laminin-type module	0	DIRECT
POU-specific domain	0	DIRECT
Tetramerization domain of potassium channels	0	DIRECT
Armadillo repeat	0	DIRECT
Mob1/phocein	0	DIRECT
Smc hinge domain	0	DIRECT
SAP domain	0	DIRECT
Integrin domains	0	DIRECT
Cell cycle control phosphatase, catalytic domain	0	DIRECT
2Fe-2S ferredoxin domains from multidomain proteins	0	DIRECT
Zf-UBP	0	DIRECT
Cullin repeat	0	DIRECT
cAMP-binding domain	0	DIRECT
Arrestin/Vps26-like	0	DIRECT
Prefoldin	0	DIRECT
MIR domain	0	DIRECT
Ankyrin repeat	0.01246	INHERITED FROM: ventral multidendritic neuron || Johnston organ neuron
Double-stranded RNA-binding domain (dsRBD)	0.07455	INHERITED FROM: germline cell
Spectrin repeat	0.09687	INHERITED FROM: fat cell || copper cell || oocyte || enterocyte
Protein kinases, catalytic subunit	0.1382	INHERITED FROM: photoreceptor cell R8 of pale ommatidium || somatic cell of ovariole || intestinal stem cell
Phoshoinositide 3-kinase (PI3K), catalytic domain	0.1628	INHERITED FROM: intestinal stem cell
Ubiquitin-related	0.2057	INHERITED FROM: mushroom body extrinsic neuron
Transducin (alpha subunit), insertion domain	0.2105	INHERITED FROM: eo neuron
Calponin-homology domain, CH-domain	0.2242	INHERITED FROM: indirect flight muscle || flight muscle
I set domains	0.2324	INHERITED FROM: gustatory system neuron || mechanosensory system neuron || pacemaker neuron || adult descending neuron || visceral muscle fiber || interface glial cell || embryonic/larval lateral glial cell || cardioblast || LNv neuron || leg taste bristle chemosensory neuron || embryonic somatic muscle || embryonic cardioblast || larval abdominal sensory neuron || s-LNv neuron || gustatory receptor neuron || embryonic heart cardioblast || adult pacemaker neuron
RecA protein-like (ATPase-domain)	0.2733	INHERITED FROM: female germline cell || nurse cell || presumptive oocyte || oocyte
SMAD domain	0.2733	INHERITED FROM: female germline stem cell || germline stem cell
ZZ domain	0.2733	INHERITED FROM: indirect flight muscle || skeletal muscle of mesothorax || flight muscle || skeletal muscle of thorax || adult somatic muscle
Homeodomain	0.2855	INHERITED FROM: A1-7 ventral acute muscle 1 || EL neuron || maxillary palp olfactory receptor neuron || dorsal margin photoreceptor || hypodermal muscle of prothorax || interneuron || ventral intersegmental muscle || thoracic neuroblast || U neuron || embryonic neuroblast || prothoracic ventral intersegmental muscle || embryonic/larval neuron || uniglomerular antennal lobe projection neuron
PDZ domain	0.3054	INHERITED FROM: somatic cell of ovariole
Cap-Gly domain	0.3532	INHERITED FROM: interneuron
Choline/Carnitine O-acyltransferase	0.3532	INHERITED FROM: skeletal muscle of mesothorax || flight muscle || somatic muscle || syncytium || skeletal muscle of thorax || adult somatic muscle
Motor proteins	0.3532	INHERITED FROM: germline cell
Cadherin	0.37	INHERITED FROM: photoreceptor cell R4 || outer photoreceptor cell
PLC-like (P variant)	0.37	INHERITED FROM: larval dorsal multidendritic neuron ddaC || larval dorsal multidendritic neuron || head mesoderm derived embryonic hemocyte
Fibronectin type III	0.374	INHERITED FROM: pacemaker neuron || LN period neuron || LNv neuron || s-LNv neuron || gustatory receptor neuron || embryonic heart cardioblast || adult pacemaker neuron
EGF-type module	0.4537	INHERITED FROM: pigment cell || embryonic/larval midgut cell || adult midgut progenitor cell || hub cell || embryonic pericardial cell || head mesoderm derived embryonic hemocyte || dorsal acute muscle
Paired domain	0.5035	INHERITED FROM: EL neuron || EG neuron || RP2 motor neuron || U neuron
Cyclin	0.5035	INHERITED FROM: female germline cell
Caspase catalytic domain	0.5395	INHERITED FROM: peptidergic neuron
HLH, helix-loop-helix DNA-binding domain	0.542	INHERITED FROM: EL neuron || sensory mother cell || 5-6I of thorax
Nuclear receptor ligand-binding domain	0.571	INHERITED FROM: supraesophageal ganglion neuron || mushroom body intrinsic neuron || interneuron
Nuclear receptor	0.5931	INHERITED FROM: supraesophageal ganglion neuron || mushroom body intrinsic neuron || interneuron
G proteins	0.681	INHERITED FROM: hemocyte
Cytochrome P450	0.6813	INHERITED FROM: neuropil associated CNS glial cell || CNS glial cell || midline glial cell || embryonic/larval glial cell || larval VNC neuropil glial cell || larval neuropil glial cell
Growth factor receptor domain	0.7527	INHERITED FROM: embryonic hemocyte || head mesoderm derived embryonic hemocyte || somatic cell of testis
Forkhead DNA-binding domain	0.818	INHERITED FROM: RP2sib neuron
Hairy Orange domain	0.8232	INHERITED FROM: EL neuron || EG neuron
SH2 domain	0.8606	INHERITED FROM: photoreceptor cell || rhabdomeric photoreceptor cell || histaminergic neuron || photoreceptor cell R7 || cyst progenitor cell || sensory organ cell || adult optic lobe neuron
FYVE, a phosphatidylinositol-3-phosphate binding domain	0.8756	INHERITED FROM: 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)
Metal cation-transporting ATPase, ATP-binding domain N	0	DIRECT
Tubulin nucleotide-binding domain-like	0	DIRECT
Smc hinge domain	0	DIRECT
SMAD MH1 domain	0	DIRECT
Sec1/munc18-like (SM) proteins	0	DIRECT
Cytokine	0	DIRECT
GINS helical bundle-like	0	DIRECT
MIR domain	0	DIRECT
NAD kinase/diacylglycerol kinase-like	0	DIRECT
Plexin repeat	0	DIRECT
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	0	DIRECT
Tropomyosin	0	DIRECT
Rhodanese/Cell cycle control phosphatase	0	DIRECT
Terpenoid synthases	0	DIRECT
SAP domain	0	DIRECT
NHL repeat	0	DIRECT
PapD-like	0	DIRECT
alpha-catenin/vinculin-like	0	DIRECT
Class II aaRS ABD-related	0	DIRECT
Arginase/deacetylase	0	DIRECT
Frizzled cysteine-rich domain	0	DIRECT
Tubulin C-terminal domain-like	0	DIRECT
post-AAA+ oligomerization domain-like	0	DIRECT
Ribosomal protein S5 domain 2-like	0	DIRECT
TIMP-like	0	DIRECT
YVTN repeat-like/Quinoprotein amine dehydrogenase	0	DIRECT
Cullin homology domain	0	DIRECT
RNase III domain-like	0	DIRECT
Metallo-hydrolase/oxidoreductase	0	DIRECT
Ferritin-like	0	DIRECT
Snake toxin-like	0	DIRECT
Cullin repeat-like	0	DIRECT
PriA/YqbF domain	0	DIRECT
Sema domain	0	DIRECT
B-box zinc-binding domain	0	DIRECT
t-snare proteins	0	DIRECT
Aminoacid dehydrogenase-like, N-terminal domain	0	DIRECT
Prefoldin	0	DIRECT
YWTD domain	0	DIRECT
CAD & PB1 domains	0	DIRECT
lambda repressor-like DNA-binding domains	0	DIRECT
Mob1/phocein	0	DIRECT
Integrin domains	0	DIRECT
Concanavalin A-like lectins/glucanases	0.0007655	DIRECT
Ankyrin repeat	0.009063	INHERITED FROM: Johnston organ neuron
p53-like transcription factors	0.01278	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte
dsRNA-binding domain-like	0.03008	INHERITED FROM: BAmv3 lineage neuron || projection neuron || antennal lobe projection neuron adPN || persistent antennal lobe projection neuron || uniglomerular antennal lobe projection neuron || mushroom body intrinsic neuron || alpha/beta Kenyon cell || Kenyon cell || adult uniglomerular antennal lobe projection neuron adPN || mushroom body extrinsic neuron || unilateral ACT relay interneuron || adult antennal lobe projection neuron adPN || adult antennal lobe projection neuron || medial antennal lobe tract projection neuron || germline cell || female germline stem cell || adult MBp lineage neuron || antennal lobe projection neuron || cholinergic neuron || adult antennal lobe projection neuron DL1 adPN
Homeodomain-like	0.04863	INHERITED FROM: dorsal margin photoreceptor || embryonic neuroblast || hypodermal muscle of prothorax || A1-7 ventral acute muscle 1 || uniglomerular antennal lobe projection neuron || prothoracic ventral intersegmental muscle || EL neuron || U neuron || muscle cell || syncytium || embryonic/larval neuron || interneuron || thoracic neuroblast
Protein kinase-like (PK-like)	0.05701	INHERITED FROM: photoreceptor cell R8 of pale ommatidium || intestinal stem cell || somatic cell of ovariole
EGF/Laminin	0.0715	INHERITED FROM: tendon cell || embryonic/larval midgut cell || embryonic/larval somatic muscle || sensory neuron || sensory organ cell || eye photoreceptor cell stalk || pericardial cell || abdominal 6 dorsal acute muscle 1 || glial cell || muscle cell || pigment cell || hypodermal muscle of larval abdominal 4 || adult midgut progenitor cell || abdominal 3 dorsal acute muscle 1 || nephrocyte || hypodermal muscle of larval abdominal 3 || syncytium || A1-7 ventral longitudinal muscle 1 || abdominal 2 dorsal acute muscle 1 || hub cell || abdominal 7 dorsal acute muscle 1 || abdominal 4 dorsal acute muscle 1 || somatic muscle || ventral longitudinal muscle || abdominal 5 dorsal acute muscle 1
E set domains	0.07323	INHERITED FROM: head mesoderm derived embryonic hemocyte || embryonic hemocyte
Spectrin repeat	0.09092	INHERITED FROM: fat cell || enterocyte || oocyte || copper cell
RING/U-box	0.09109	INHERITED FROM: garland cell || embryonic/larval garland cell
BAR/IMD domain-like	0.1246	INHERITED FROM: bouton || synapse || NMJ bouton
Actin depolymerizing proteins	0.1555	INHERITED FROM: follicle cell
Transducin (alpha subunit), insertion domain	0.2027	INHERITED FROM: eo neuron
L domain-like	0.2037	INHERITED FROM: BAlc1 lineage neuron
Calponin-homology domain, CH-domain	0.2073	INHERITED FROM: flight muscle || indirect flight muscle
Immunoglobulin	0.2213	INHERITED FROM: pacemaker neuron || adult pacemaker neuron || LNv neuron || cardioblast || embryonic cardioblast || longitudinal muscle || glial cell || LN period neuron || embryonic heart cardioblast || leg taste bristle chemosensory neuron
PAZ domain	0.2655	INHERITED FROM: pole cell
Cadherin-like	0.292	INHERITED FROM: photoreceptor cell R4
Fibronectin type III	0.3358	INHERITED FROM: pacemaker neuron || dendritic arborizing neuron || adult pacemaker neuron || LNv neuron || embryonic cardioblast || s-LNv neuron || LN period neuron || embryonic heart cardioblast || leg taste bristle chemosensory neuron
Cap-Gly domain	0.347	INHERITED FROM: interneuron
ENTH/VHS domain	0.4363	INHERITED FROM: imaginal disc epithelial cell
Caspase-like	0.4363	INHERITED FROM: interommatidial precursor cell || peptidergic neuron
HAD-like	0.4552	INHERITED FROM: rhabdomere of eye photoreceptor cell
Metalloproteases ("zincins"), catalytic domain	0.4564	INHERITED FROM: embryonic cardioblast || embryonic heart cardioblast
SMAD/FHA domain	0.4874	INHERITED FROM: female germline stem cell
HLH, helix-loop-helix DNA-binding domain	0.4954	INHERITED FROM: 5-6I of thorax || EL neuron || sensory mother cell
CoA-dependent acyltransferases	0.5285	INHERITED FROM: flight muscle || adult somatic muscle || skeletal muscle of thorax || skeletal muscle of mesothorax
Nuclear receptor ligand-binding domain	0.5452	INHERITED FROM: mushroom body intrinsic neuron || supraesophageal ganglion neuron || interneuron
Cytochrome P450	0.6631	INHERITED FROM: CNS glial cell || midline glial cell || larval neuropil glial cell || embryonic/larval glial cell || neuropil associated CNS glial cell || larval VNC neuropil glial cell
Cyclin-like	0.6736	INHERITED FROM: female germline cell
Growth factor receptor domain	0.6829	INHERITED FROM: head mesoderm derived embryonic hemocyte || photoreceptor cell R7 || GABAergic neuron || dMP2 neuron || vMP2 neuron || RP2sib neuron || surface associated glial cell || stage 1 neuroblast || dorsal acute muscle || pigment cell || retinal pigment cell || neuroblast of ventral nerve cord primordium || somatic cell of testis || embryonic hemocyte || neuroblast NB5-2
Orange domain-like	0.7368	INHERITED FROM: 5-6I of thorax || 5-6I || EL neuron || EG neuron || thoracic neuron
Tetraspanin	0.8097	INHERITED FROM: sensory mother cell
SH2 domain	0.8366	INHERITED FROM: rhabdomeric photoreceptor cell || photoreceptor cell R7 || adult optic lobe neuron || sensory organ cell || histaminergic neuron || cyst progenitor cell || photoreceptor cell
beta-beta-alpha zinc fingers	1	INHERITED FROM: 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)
101912,103575 101912 - Sema domain 103575 - Plexin repeat	0	DIRECT
57196,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases	0	DIRECT
57903,47370 57903 - FYVE/PHD zinc finger 47370 - Bromodomain	0	DIRECT
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat	0	DIRECT
49417,81296 49417 - p53-like transcription factors 81296 - E set domains	0	DIRECT
48403,48403 48403 - Ankyrin repeat 48403 - Ankyrin repeat	0	DIRECT
55753,55753 55753 - Actin depolymerizing proteins 55753 - Actin depolymerizing proteins	0	DIRECT
47220,47220 47220 - alpha-catenin/vinculin-like 47220 - alpha-catenin/vinculin-like	0	DIRECT
49899,49899 49899 - Concanavalin A-like lectins/glucanases 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
54534,48452 54534 - FKBP-like 48452 - TPR-like	0	DIRECT
49899,57196 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin	0	DIRECT
47459,55785 47459 - HLH, helix-loop-helix DNA-binding domain 55785 - PYP-like sensor domain (PAS domain)	0	DIRECT
75632,46785 75632 - Cullin homology domain 46785 - "Winged helix" DNA-binding domain	0	DIRECT
63748,63748 63748 - Tudor/PWWP/MBT 63748 - Tudor/PWWP/MBT	0	DIRECT
74788,75632 74788 - Cullin repeat-like 75632 - Cullin homology domain	0	DIRECT
81660,56784 81660 - Metal cation-transporting ATPase, ATP-binding domain N 56784 - HAD-like	0	DIRECT
81296,81296 81296 - E set domains 81296 - E set domains	0	DIRECT
47413,46689 47413 - lambda repressor-like DNA-binding domains 46689 - Homeodomain-like	0	DIRECT
52540,48019 52540 - P-loop containing nucleoside triphosphate hydrolases 48019 - post-AAA+ oligomerization domain-like	0	DIRECT
52490,55307 52490 - Tubulin nucleotide-binding domain-like 55307 - Tubulin C-terminal domain-like	0	DIRECT
54768,54768 54768 - dsRNA-binding domain-like 54768 - dsRNA-binding domain-like	0	DIRECT
51206,51206 51206 - cAMP-binding domain-like 51206 - cAMP-binding domain-like	0	DIRECT
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin	0.117	INHERITED FROM: rhabdomeric photoreceptor cell || embryonic/larval pericardial cell || embryonic/larval somatic muscle || sensory organ cell || eye photoreceptor cell stalk || pericardial cell || secondary pigment cell || nephrocyte || hub cell || tertiary pigment cell
48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin	0.1361	INHERITED FROM: pacemaker neuron || interommatidial precursor cell || adult pacemaker neuron || LNv neuron || cardioblast || embryonic cardioblast || longitudinal muscle || embryonic somatic muscle || s-LNv neuron || LN period neuron || embryonic heart cardioblast || leg taste bristle chemosensory neuron
47895,52540 47895 - Transducin (alpha subunit), insertion domain 52540 - P-loop containing nucleoside triphosphate hydrolases	0.2027	INHERITED FROM: eo neuron
49562,49562 49562 - C2 domain (Calcium/lipid-binding domain, CaLB) 49562 - C2 domain (Calcium/lipid-binding domain, CaLB)	0.347	INHERITED FROM: bouton || synapse
52777,52777 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases	0.347	INHERITED FROM: flight muscle || adult somatic muscle || skeletal muscle of thorax || skeletal muscle of mesothorax || muscle cell || syncytium || somatic muscle
55550,50044 55550 - SH2 domain 50044 - SH3-domain	0.347	INHERITED FROM: photoreceptor cell R7 || inner photoreceptor cell
49313,49313 49313 - Cadherin-like 49313 - Cadherin-like	0.358	INHERITED FROM: photoreceptor cell R4 || outer photoreceptor cell
49265,49265 49265 - Fibronectin type III 49265 - Fibronectin type III	0.4363	INHERITED FROM: larval abdominal sensory neuron || abdominal neuron || dendritic arborizing neuron || multidendritic neuron
48726,49265 48726 - Immunoglobulin 49265 - Fibronectin type III	0.5103	INHERITED FROM: pacemaker neuron || gustatory receptor neuron || mechanosensory neuron || adult pacemaker neuron || LNv neuron || chemosensory neuron || giant fiber neuron || chemosensory system neuron || adult descending neuron || neuropil associated CNS glial cell || s-LNv neuron || LN period neuron || embryonic heart cardioblast || leg taste bristle chemosensory neuron
50978,50978 50978 - WD40 repeat-like 50978 - WD40 repeat-like	0.565	INHERITED FROM: mechanosensory system neuron || mechanosensory neuron
47954,47954 47954 - Cyclin-like 47954 - Cyclin-like	0.6631	INHERITED FROM: female germline cell
47459,158457 47459 - HLH, helix-loop-helix DNA-binding domain 158457 - Orange domain-like	0.7368	INHERITED FROM: 5-6I of thorax || 5-6I || EL neuron || EG neuron || thoracic neuron
47473,47473 47473 - EF-hand 47473 - EF-hand	0.7379	INHERITED FROM: bouton
57196,57184 57196 - EGF/Laminin 57184 - Growth factor receptor domain	0.8259	INHERITED FROM: head mesoderm derived embryonic hemocyte || photoreceptor cell R7 || pigment cell || inner photoreceptor cell || crystal cell || somatic cell of testis || hub cell || 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)
57850,57850,57850 57850 - RING/U-box 57850 - RING/U-box 57850 - RING/U-box	0	DIRECT
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	DIRECT
57196,49899,49899 57196 - EGF/Laminin 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases	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
74788,75632,46785 74788 - Cullin repeat-like 75632 - Cullin homology domain 46785 - "Winged helix" DNA-binding domain	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
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains	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
48452,48452,48452 48452 - TPR-like 48452 - TPR-like 48452 - TPR-like	0	DIRECT
57196,57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin 57196 - EGF/Laminin	0.04015	INHERITED FROM: rhabdomeric photoreceptor cell || head mesoderm derived embryonic hemocyte || embryonic/larval pericardial cell || adult optic lobe neuron || embryonic/larval somatic muscle || sensory neuron || embryonic/larval hypodermal muscle || sensory organ cell || eye photoreceptor cell stalk || pericardial cell || histaminergic neuron || glial cell || secondary pigment cell || nephrocyte || photoreceptor cell R6 || somatic cell of testis || hub cell || photoreceptor cell R1 || embryonic hemocyte || tertiary pigment cell
48726,48726,49265 48726 - Immunoglobulin 48726 - Immunoglobulin 49265 - Fibronectin type III	0.2917	INHERITED FROM: mechanosensory system neuron || pacemaker neuron || gustatory receptor neuron || mechanosensory neuron || adult pacemaker neuron || LNv neuron || chemosensory neuron || giant fiber neuron || eo neuron || chemosensory system neuron || adult descending neuron || neuropil associated CNS glial cell || s-LNv neuron || LN period neuron || embryonic heart cardioblast || leg taste bristle chemosensory neuron
48726,48726,48726 48726 - Immunoglobulin 48726 - Immunoglobulin 48726 - Immunoglobulin	0.3507	INHERITED FROM: pacemaker neuron || interommatidial precursor cell || gustatory receptor neuron || adult pacemaker neuron || LNv neuron || embryonic cardioblast || embryonic/larval garland cell || s-LNv neuron || interneuron || embryonic heart cardioblast || leg taste bristle chemosensory neuron
49313,49313,49313 49313 - Cadherin-like 49313 - Cadherin-like 49313 - Cadherin-like	0.358	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.