Tools — Live Ranking

Every external database / API / server / software / viewer / model used in STRC research. Each card answers: what it does, how to use it, when, and which hypothesis cited it. Schema: ~/STRC/_templates/fileclasses/tool.md.

Rubric

Tiers mirror the STRC Hypothesis Ranking:

S — actively used in current proofs; results cited in a hub
A — verified working on STRC inputs; ready when needed
B — described, never run on STRC variant
C — stub / unverified
D — superseded, deprecated, or persistently broken (kept for replication)

Status (status:) is operational state — orthogonal to tier. A B-tier tool can be active; an S-tier one can be broken.

Curated narrative map by research task: Genomics & Bioinformatics Tools.

S-tier — driving active proofs

TABLE WITHOUT ID
  file.link AS "Tool",
  kind AS "Kind",
  category AS "Category",
  hypotheses_used AS "Used by",
  last_used AS "Last used"
FROM "tools"
WHERE tier = "S"
SORT last_used DESC, file.name ASC

Tool	Kind	Category	Used by	Last used
RDKit	database	pharmacology	h01	2026-04-26
ADMET-AI	database	pharmacology	h01	2026-04-24
APBS	database	structure	h01	2026-04-24
AlphaFold 3 Server	server	structure	h01	2026-04-08

A-tier — verified, ready

TABLE WITHOUT ID
  file.link AS "Tool",
  kind AS "Kind",
  category AS "Category",
  hypotheses_used AS "Used by",
  last_used AS "Last used"
FROM "tools"
WHERE tier = "A"
SORT file.name ASC

Tool	Kind	Category	Used by	Last used
AAV Capsid Database	database	delivery
ASGCT Gene Therapy Database	database	delivery
AlphaFold Database	server	structure
AlphaGenome	model	variant-effect	h01	2026-04-08
AlphaMissense	database	structure
BRAVO — TOPMed	database	population
CADD	database	misc
CIViC	database	clinical
ClinGen	database	misc
ClinVar	database	misc
ClinicalTrials.gov	database	delivery
Clustal Omega	database	conservation
DECIPHER	database	population
Deafness Variation Database	database	misc
ENCODE	database	regulatory
ESMFold	server	structure
Ensembl REST API	api	misc
Franklin	database	misc
Hereditary Hearing Loss Homepage	database	misc
Human Protein Atlas	database	misc
IUPred3	server	structure
InterVar	database	misc
LOVD	database	population
LitVar 2.0	database	literature
Mol Star Viewer	viewer	structure
Mutalyzer	database	misc
NetGPI	database	misc
NetNGlyc	database	misc
OMIM	database	misc
Open Targets	database	clinical
OrthoDB	database	conservation
PubMed	database	literature
REVEL	database	misc
RegulomeDB	database	regulatory
SWISS-MODEL	server	structure
Semantic Scholar	database	literature
SignalP	database	misc
UCSC Genome Browser	viewer	regulatory
UniProt	database	conservation
VarSome	database	misc
dbNSFP	database	misc
gnomAD	database	population
seqr	database	population

B-tier — described, untested on STRC

TABLE WITHOUT ID
  file.link AS "Tool",
  kind AS "Kind",
  category AS "Category",
  acmg AS "ACMG",
  url AS "URL"
FROM "tools"
WHERE tier = "B"
SORT category ASC, file.name ASC

Tool	Kind	Category	ACMG	URL
HGMD Professional	database	clinical	PS4, PM5, PP5	https://www.hgmd.cf.ac.uk/
Mastermind	database	clinical	PS4, PM5	https://mastermind.genomenon.com/
PharmGKB	database	clinical		https://www.pharmgkb.org/
ConSurf	database	conservation	PP3	http://consurf.tau.ac.il/
EVcouplings	database	conservation	PP3	https://evcouplings.org/
Caduceus	model	foundation-model	PP3	https://github.com/kuleshov-group/caduceus
DNABERT-2	model	foundation-model	PP3	https://github.com/MAGICS-LAB/DNABERT_2
Evo — Evo 2	model	foundation-model	PP3	https://arcinstitute.org/tools/evo
HyenaDNA	model	foundation-model	PP3	https://github.com/HazyResearch/hyena-dna
Nucleotide Transformer (NTv3)	model	foundation-model	PP3	https://github.com/instadeepai/nucleotide-transformer
PubTator	database	literature		https://www.ncbi.nlm.nih.gov/research/pubtator/
Allen Brain Atlas	database	misc		https://brain-map.org/
AnnotSV	database	misc	ACMG 2019 (CNV)	https://lbgi.fr/AnnotSV/
AudioGene	database	misc	PP4	https://audiogene.eng.uiowa.edu/
CNest	database	misc		https://github.com/tf2/CNest (original link pointed to generic broadinstitute org — fixed)
ClassifyCNV	database	misc	ACMG 2019 (CNV)	https://github.com/Genotek/ClassifyCNV
DB-OTO Trial Resources	database	misc		https://www.packgene.com/
Delly	database	misc		https://github.com/dellytools/delly
Expression Atlas	database	misc		https://www.ebi.ac.uk/gxa/
Galaxy Project	database	misc		https://usegalaxy.org/
HIEDRA	database	misc		https://explore.data.humancellatlas.org/
Manta	database	misc		https://github.com/Illumina/manta
Sensorion AAV Platform	database	misc		https://www.sensorion.com/
Terra.bio	database	misc		https://terra.bio/
VariantValidator	database	misc		https://variantvalidator.org/
gEAR	database	misc		https://umgear.org/
variant tools (vtools)	database	misc		https://bio.tools/vtools
Biobank Japan (BBJ) — PheWeb	database	population	BA1, BS1, PM2	https://pheweb.jp/
CMDB (Chinese Millionome)	database	population	BA1, BS1, PM2	https://db.cngb.org/cmdb/
KoB — KDNA	database	population	BA1, BS1, PM2	https://www.biobigdata.kr/
dbSNP	database	population	BA1, BS1, PM2	https://www.ncbi.nlm.nih.gov/snp/
Basenji	database	regulatory	PP3	https://github.com/calico/basenji
DeepSEA	database	regulatory	PP3	https://hb.flatironinstitute.org/
Enformer	database	regulatory	PP3	https://github.com/google-deepmind/deepmind-research (org renamed: deepmind → google-deepmind)
AbSplice2	database	splicing	PP3	https://absplice.cmm.cit.tum.de
FRASER2	database	splicing	PS3, BS3	https://github.com/gagneurlab/FRASER
MMSplice	database	splicing	PP3	https://github.com/gagneurlab/MMSplice_MTSplice (repo renamed from MMSplice)
MaxEntScan	database	splicing	PP3	~~https://github.com/gagneurlab/splicemodels~~ BROKEN — repo does not exist
Pangolin	database	splicing	PP3	https://github.com/bw2/Pangolin
SpliceAI	database	splicing
DDGun — DDGun3D	server	structure	PP3	https://github.com/biofold/ddgun
DynaMut	server	structure	PP3	https://biosig.lab.uq.edu.au/dynamut/
FoldX	server	structure	PP3	http://foldxsuite.crg.eu/
MRGPRX2 AF-M screen	database	structure
PyMOL	database	structure
RoseTTAFold	server	structure	PM1, PP3	https://github.com/RosettaCommons/RoseTTAFold
mCSM	server	structure	PP3	https://biosig.lab.uq.edu.au/mcsm/
BayesDel	database	variant-effect	PP3	~~https://github.com/broadinstitute/dbnsfp~~ BROKEN — repo does not exist
DANN	database	variant-effect	PP3	~~https://github.com/michoel-lab/dann~~ BROKEN — repo does not exist
ESM1v	database	variant-effect	PP3, BP4	https://github.com/facebookresearch/esm
EVE (Evolutionary model of Variant Effect)	database	variant-effect	PP3, BP4	https://evemodel.org/
Eigen — Eigen-PC	database	variant-effect	PP3	http://www.columbia.edu/~ii2135/eigen.html
PrimateAI-3D	database	variant-effect	PP3, PM1	https://github.com/Illumina/PrimateAI-3D
gMVP	database	variant-effect	PP3	https://github.com/ShenLab/gMVP

C-tier — stub / unverified

TABLE WITHOUT ID
  file.link AS "Tool",
  category AS "Category",
  acmg AS "ACMG",
  url AS "URL"
FROM "tools"
WHERE tier = "C"
SORT category ASC, file.name ASC

Tool	Category	ACMG	URL
CGAR	clinical	PM2, PS4	https://cgar.org/
DGIdb	clinical		https://www.dgidb.org/
GWAS Catalog	clinical		https://www.ebi.ac.uk/gwas/
PhastCons	conservation	PP3	http://compgen.cshl.edu/phast/
PhyloP	conservation	PP3	http://compgen.cshl.edu/phast/
Rate4Site	conservation	PP3	http://consurf-hssp.tau.ac.il/
Amazon BioDiscovery and AWS HealthOmics	delivery
Europe PMC	literature		https://europepmc.org/
LitSense	literature		https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/
LitSuggest	literature		https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/
tmVar	literature		https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/
ARCHS4	misc		https://archs4.org/
CNVnator	misc		https://github.com/abyzovlab/CNVnator
CrossMap	misc		https://crossmap.sourceforge.net/
EVEE Evo Variant Effect Explorer	misc
GATK gCNV	misc		https://gatk.broadinstitute.org/
Illumina Connected Insights	misc		https://www.illumina.com/
UCSC LiftOver	misc		https://genome.ucsc.edu/cgi-bin/hgLiftOver
AmberTools	molecular-dynamics
GROMACS	molecular-dynamics
OpenMM	molecular-dynamics
RAMD-OpenMM	molecular-dynamics
gmx_MMPBSA	molecular-dynamics		https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA
ALFA	population	BA1, BS1, PM2	https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/
ClinGen Allele Registry	population		https://reg.clinicalgenome.org/
UK Biobank	population	BA1, BS1, PM2	https://www.ukbiobank.ac.uk/
GTEx Portal	regulatory	PM2	https://gtexportal.org/
HaploReg	regulatory	PP3	https://pubs.broadinstitute.org/mammals/haploreg/
Roadmap Epigenomics	regulatory	PP3	https://epigenomesportal.ca/
GeneSplicer	splicing	PP3	https://ccb.jhu.edu/software/genesplicer/
NNSplice	splicing	PP3	https://www.fruitfly.org/seq_tools/splice.html
SPANR	splicing	PP3	http://tools.genes.toronto.edu/
SPiP	splicing	PP3	https://sourceforge.net/projects/splicing-prediction-pipeline/
DUET	structure	PP3	https://biosig.lab.uq.edu.au/duet/
ELASPIC	structure	PP3	http://elaspic.kimlab.org/
IFUM	structure	PP3	https://github.com/HParklab/IFUM
RosettaDDG	structure	PP3	https://github.com/ELELAB/RosettaDDGPrediction
SDM	structure	PP3	https://biosig.lab.uq.edu.au/sdm/
boltz-2	structure
ClinPred	variant-effect	PP3	https://sites.google.com/site/clinpred/
FATHMM-MKL	variant-effect	PP3	http://fathmm.biocompute.org.uk/
GERP++	variant-effect	PP3	http://mendel.stanford.edu/SidowLab/downloads/gerp/
LINSIGHT	variant-effect	PP3	http://compgen.cshl.edu/
MPC	variant-effect	PP3	https://broadinstitute.org/
SnpEff	variant-effect		https://pcingola.github.io/SnpEff/
fitCons	variant-effect	PP3	http://compgen.cshl.edu/fitCons/

D-tier — superseded, deprecated, or broken

TABLE WITHOUT ID
  file.link AS "Tool",
  status AS "Status",
  superseded_by AS "Replaced by",
  url AS "URL"
FROM "tools"
WHERE tier = "D"
SORT status ASC, file.name ASC

Tool	Status	Replaced by	URL
FAVOR	broken		~~https://favor.genohub.org/~~ 500 SERVER ERROR (2026-04-09)
HAL	broken		~~https://hal.mdc-berlin.de/~~ SITE DOWN (ECONNREFUSED as of 2026-04-09)
MetaRNN	broken		~~https://vep.varianteffect.org/~~ SITE DOWN (ECONNREFUSED as of 2026-04-09)
MutScore	broken		~~https://github.com/mutscore~~ BROKEN — GitHub org does not exist
PIQ	broken		~~https://github.com/Yuanlab/PIQ~~ BROKEN — repo does not exist
PoPMuSiC	broken		~~https://soft.vub.ac.be/popmusic/~~ 404 NOT FOUND (2026-04-09)
SAGE	broken		~~https://sage.igib.in/~~ SITE DOWN (ECONNREFUSED as of 2026-04-09)
STRUM	broken		~~https://zhanggroup.org/STRUM/~~ REDIRECTS to https://aideepmed.com/STRUM/ (403 forbidden, 2026-04-09)
SparkINFERNO	broken		~~https://cardio-care.shinyapps.io/VEP_Finder/~~ SHINY APP DOWN (2026-04-09)
SpliceRover	broken		~~https://github.com/cibiobcg/SpliceRover~~ BROKEN — repo does not exist
TLand	broken		~~https://github.com/Weng-Lab/TLand~~ BROKEN — repo does not exist
VEST4	broken		~~https://karchinlab.org/apps/appVest.html~~ 404 NOT FOUND (2026-04-09)
fpocket	broken
ExAC (Legacy)	superseded	gnomAD	https://exac.broadinstitute.org/
GERP	superseded	GERP++	http://mendel.stanford.edu/

Roll-up by category

TABLE WITHOUT ID
  category AS "Category",
  length(rows) AS "Count",
  filter(rows.file.name, (n) => n != null) AS "Tools"
FROM "tools"
WHERE type = "tool" AND file.name != "index" AND file.name != "Genomics & Bioinformatics Tools"
GROUP BY category
SORT category ASC

(no results)

Lint — cards missing canonical fields

Cards still on the legacy type: note schema or missing tier/excerpt. Should be 0 after migration; new entries that drift land here.

TABLE WITHOUT ID
  file.link AS "Tool",
  type AS "Type",
  tier AS "Tier",
  excerpt AS "Excerpt"
FROM "tools"
WHERE file.name != "index" AND file.name != "Genomics & Bioinformatics Tools"
  AND (type != "tool" OR !tier OR !excerpt)
SORT file.name ASC