Database statistics
Phylum/Class/Order/Family/Speices7/15/35/42/68
Fully annotated/Chromosome-level genomes46/22
Tracks in Jbrowse401
Paleobiological records1,413
Busco genes16,015
Protein-Coding Genes1,449,954
Transcriptomic Datasets950
Sing-cell RNA-seq Datasets15
Metagenomic Datasets1,112
Symbiotic Microorganism Datasets/annotation41/92,682
Co-expressed networks/positive/negative gene pairs6/1,485,344/520,014
Cell types14
Cell markers1,793
GO/KEGG/Pfam/Panther/Interpro annotation3,606,859/18,539/1,281,713/928,123/3,640,096
TFs/Ubiquitin families60,866/82,844


  Softwares
ModuleSoftwareParameterLinks
Fossil recordsPBDB and WoRDDSdefaulthttps://paleobiodb.org/#/
https://www.marinespecies.org/deepsea/index.php
Gene annotationInterProScan v.5.67-97.0-f tsv -goterms -pahttps://github.com/ebi-pf-team/interproscan
Busco GeneBUSCO v.5.8.2-l metazoa_odb12 -m proteinshttps://gitlab.com/ezlab/busco
TFs/UbsHMMER v.3.4cut-off: 0.0001http://hmmer.org/
Gene FamilyOrthoFinder v.2.5.5defaulthttps://github.com/davidemms/OrthoFinder
Microsynteny AnalysisPansyn ToolkitMicrosyn_MCScanX -a diamond, Microsyn_wgdi -a diamondhttps://github.com/yhw320/PanSyn
Macrosynteny AnalysisPansyn ToolkitMacrosyn_add_species -a diamondhttps://github.com/yhw320/PanSyn
Mitogenomic DataOGDRAW v.1.3.1defaulthttps://chlorobox.mpimp-golm.mpg.de/OGDraw.html
Expression heatmapHighchartsdefaulthttps://www.highcharts.com/
Co-expression networkCytoscape v3.10.3defaulthttps://cytoscape.org/
Single-cell DataSeurat v4.4LogNormalizehttps://satijalab.org/seurat
Species treephylotreedefaulthttps://www.phylotree.org/
Primer DesignPrimer3Plusdefaulthttps://github.com/primer3-org
Database constructionLAMPdefaulthttps://github.com/teddysun/lamp
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