Database statistics| Phylum/Class/Order/Family/Speices | 7/15/35/42/68 |
|---|---|
| Fully annotated/Chromosome-level genomes | 46/22 |
| Tracks in Jbrowse | 401 |
| Paleobiological records | 1,413 |
| Busco genes | 16,015 |
| Protein-Coding Genes | 1,449,954 |
| Transcriptomic Datasets | 950 |
| Sing-cell RNA-seq Datasets | 15 |
| Metagenomic Datasets | 1,112 |
| Symbiotic Microorganism Datasets/annotation | 41/92,682 |
| Co-expressed networks/positive/negative gene pairs | 6/1,485,344/520,014 |
| Cell types | 14 |
| Cell markers | 1,793 |
| GO/KEGG/Pfam/Panther/Interpro annotation | 3,606,859/18,539/1,281,713/928,123/3,640,096 |
| TFs/Ubiquitin families | 60,866/82,844 |
Softwares| Module | Software | Parameter | Links |
|---|---|---|---|
| Fossil records | PBDB and WoRDDS | default | https://paleobiodb.org/#/ https://www.marinespecies.org/deepsea/index.php |
| Gene annotation | InterProScan v.5.67-97.0 | -f tsv -goterms -pa | https://github.com/ebi-pf-team/interproscan |
| Busco Gene | BUSCO v.5.8.2 | -l metazoa_odb12 -m proteins | https://gitlab.com/ezlab/busco |
| Transposable Elements | RepeatModeler v.2.0.7 RepeatModeler v.4.2.1 | -engine rmblast -LTRStruct -gff -e rmblast -nolow | https://github.com/Dfam-consortium/RepeatModeler https://github.com/Dfam-consortium/RepeatMasker |
| TFs/Ubs | HMMER v.3.4 | cut-off: 0.0001 | http://hmmer.org/ |
| Gene Family | OrthoFinder v.2.5.5 | default | https://github.com/davidemms/OrthoFinder |
| Pan-geneset | Count | Wagner_parsimony -gain 1 -max_paralogs 200 Posteriors -max_paralogs 200 | https://www.iro.umontreal.ca/~csuros/gene_content/count.html |
| Microsynteny Analysis | Pansyn Toolkit | Microsyn_MCScanX -a diamond Microsyn_wgdi -a diamond | https://github.com/yhw320/PanSyn |
| Macrosynteny Analysis | Pansyn Toolkit | Macrosyn_add_species -a diamond | https://github.com/yhw320/PanSyn |
| Mitogenomic Data | OGDRAW v.1.3.1 | default | https://chlorobox.mpimp-golm.mpg.de/OGDraw.html |
| Expression heatmap | Highcharts | default | https://www.highcharts.com/ |
| Co-expression network | Cytoscape v3.10.3 | default | https://cytoscape.org/ |
| Single-cell Data | Seurat v4.4 | LogNormalize | https://satijalab.org/seurat |
| Species tree | phylotree | default | https://www.phylotree.org/ |
| Primer Design | Primer3Plus | default | https://github.com/primer3-org |
| Database construction | LAMP | default | https://github.com/teddysun/lamp |
