EcoSeek

EcoSeek Genominer

Population-genetic candidate species, reference genomes, and clean VCFs for landscape-genetic / refugia analyses.

135
Candidates
9
SPA-ready
35
VCF files
24
Species with VCF

VCF performance

VCF files per species

Facets

Genus Quercus (23)Pinus (12)Sciurus (6)Bombus (6)Microtus (4)Lycaena (4)Lepus (4)Juglans (4)Tsuga (3)Populus (3)Plethodon (3)Picea (3)Odocoileus (3)Coenonympha (3)Speyeria (2)
Markers microsatellite (36)mtDNA (29)WGS (27)SNP (20)microsatellite,mtDNA (9)RADseq (5)WGS,mtDNA (3)SNP,mtDNA (3)WGS,microsatellite (2)SNP,WGS,mtDNA (2)SNP,STR (2)RADseq,mtDNA (2)RADseq,WGS,mtDNA (2)allozyme (1)STR (1)
Geography North America (131)Europe (119)

Species catalog

clear
SpeciesGenusScoreMarkersContinentsFlagsDownloads
Speyeria cybele Speyeria 102.0 SNP,WGS,mtDNA Europe, North America ref_genome
Speyeria leto Speyeria 102.0 SNP,WGS,mtDNA Europe, North America ref_genome

VCF files

DatasetBinomialTypeSamplesVariantsSizeDownloads
acer_saccharum Acer saccharum clean_biallelic_snps 1 9158129 325.3 MB VCFpopmapG'STmetrics
biswas2026_truculentus_wgs Thrigmopoeus truculentus clean_biallelic_snps 30 249885 20.0 MB VCFG'STFST
bombus_balteatus_wgs Bombus balteatus clean_biallelic_snps 40 7024680 589.6 MB VCFpopmapmetrics
bombus_terrestris Bombus terrestris clean_biallelic_snps 28 13612996 559.1 MB VCFpopmapG'STmetrics
bono2018_reference Sciurus aberti clean_biallelic_snps 92 125622 37.0 MB VCFFST
bono2018_reference Sciurus aberti clean_biallelic_snps 92 615320 126.8 MB VCFFST
bono2018_stacks Sciurus aberti other 92 70914 69.2 MB VCF
canis_aureus Canis aureus clean_biallelic_snps 6 13976432 466.8 MB VCFpopmapG'STmetrics
desmognathus_wrighti Desmognathus wrighti clean_biallelic_snps 14 834 2.7 MB VCFpopmapG'STmetrics
fusco2024_carolinensis_full Sciurus carolinensis clean_biallelic_snps 403 7588480 2.8 GB VCFpopmapG'STFST
fusco2024_carolinensis_pilot Sciurus carolinensis clean_biallelic_snps 50 174035 20.3 MB VCFpopmapG'STFST
fusco2024_carolinensis_pilot Sciurus carolinensis clean_biallelic_snps 50 2427587 317.3 MB VCFpopmapG'STFST
gulo_gulo Gulo gulo clean_biallelic_snps 12 1295424 53.6 MB VCFpopmapG'STmetrics
juniperus_communis Juniperus communis clean_biallelic_snps 6 2993523 75.3 MB VCFpopmapG'STmetrics
lepus_americanus Lepus americanus clean_biallelic_snps 10 35899274 1.1 GB VCFpopmapG'STmetrics
lepus_californicus Lepus californicus clean_biallelic_snps 5 72458961 2.9 GB VCFpopmapG'STmetrics
lepus_europaeus Lepus europaeus clean_biallelic_snps 3 30845573 1.1 GB VCFpopmapG'STmetrics
lepus_timidus_wgs Lepus timidus raw_variants 0 0.0 B VCFpopmap
odocoileus_hemionus_wgs Odocoileus hemionus clean_biallelic_snps 29 37427568 2.4 GB VCFpopmapmetrics
odocoileus_virginianus Odocoileus virginianus clean_biallelic_snps 30 92802336 5.8 GB VCFpopmapG'STmetrics
pinus_flexilis_strobiformis_pilot Pinus flexilis other 110 37 97.9 KB VCFpopmapG'STFST
pinus_flexilis_strobiformis_pilot Pinus flexilis stacks 110 10778 5.0 MB VCFpopmapG'STFST
pinus_flexilis_strobiformis_pilot Pinus flexilis stacks 110 10931 1.1 MB VCFpopmapG'STFST
pinus_flexilis_strobiformis_pilot Pinus flexilis stacks 110 6267 744.8 KB VCFpopmapG'STFST
pinus_pungens_rigida_pilot Pinus pungens stacks 66 7496 2.2 MB VCFpopmapG'STFST
pinus_pungens_rigida_pilot Pinus pungens stacks 66 7588 540.5 KB VCFpopmapG'STFST
pinus_pungens_rigida_pilot Pinus pungens stacks 66 20361 1.3 MB VCFpopmapG'STFST
plethodon_cinereus Plethodon cinereus clean_biallelic_snps 3 316150 25.1 MB VCFpopmapG'ST
plethodon_cinereus_wgs Plethodon cinereus raw_variants 3 2223052 63.0 MB VCFpopmapG'ST
populus_tremuloides Populus tremuloides clean_biallelic_snps 1 10522216 307.8 MB VCFpopmapG'STmetrics
quercus_canariensis_wgs Quercus canariensis clean_biallelic_snps 2 15799925 529.1 MB VCFpopmapmetrics
quercus_lobata Quercus lobata clean_biallelic_snps 34 14638769 714.0 MB VCFpopmapG'STmetrics
quercus_macrocarpa_wgs Quercus macrocarpa clean_biallelic_snps 11 30498576 1.2 GB VCFpopmapmetrics
quercus_rubra Quercus rubra clean_biallelic_snps 29 52972777 3.5 GB VCFpopmapG'STmetrics
quercus_rubra_wgs Quercus rubra other 29 693115 32.6 MB VCFpopmapG'STmetrics

API

GET /api/catalog?q=...&genus=...&has_vcf=true&limit=100

GET /api/candidates

GET /api/facets

GET /api/vcfs

GET /api/vcf_manifest.tsv

GET /api/download/<relative_path>

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