.gitignore
CHANGELOG.md
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
README_EN.md
gene.nwk.reconciled
genome.protein.fa.tbtools.json
install.sh
mkdocs.yml
pyproject.toml
requirements-ci.txt
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/docs.yml
.github/workflows/nightly-e2e.yml
.github/workflows/onboarding-e2e.yml
.github/workflows/test.yml
bin/tbcli.py
bin/tbengine.sh
bin/tbplot.sh
bin/tbtools
bin/tbtools_rpc.sh
bridges/AdmixtureCli.java
bridges/AmazingMetaCli.java
bridges/AssemblyRecommandCli.java
bridges/BamIndexCli.java
bridges/BamSortCli.java
bridges/BamStateCli.java
bridges/BarPlotterCli.java
bridges/BarplotCli.java
bridges/BatchVizMotifsCli.java
bridges/BlastXmlConvertCli.java
bridges/BlatExecutorCli.java
bridges/CalcRepeatCli.java
bridges/CalculateSimilarityCli.java
bridges/CddMotifCli.java
bridges/CircleGeneViewerCli.java
bridges/CircosCli.java
bridges/ColorSchemeCli.java
bridges/CtgGroupCli.java
bridges/CubeHeatmapCli.java
bridges/DeHistCli.java
bridges/DegramdomCli.java
bridges/DiffExpCli.java
bridges/DistanceCli.java
bridges/DualSynCli.java
bridges/EggnogCli.java
bridges/ExprCorrCli.java
bridges/FastaMergerCli.java
bridges/FastaTableConvertCli.java
bridges/FileCleanerCli.java
bridges/FileSplitCli.java
bridges/FindBlockDualCli.java
bridges/FindBlockMultipleCli.java
bridges/FindPathCli.java
bridges/GSEAWrapperCli.java
bridges/GenBank2FastaCli.java
bridges/GeneDensityCli.java
bridges/GeneLocGffCli.java
bridges/GeneStructureCli.java
bridges/GenericCli.java
bridges/GetENALinksCli.java
bridges/GetSubNewickTreeCli.java
bridges/GoEnrichCli.java
bridges/GoLevelCli.java
bridges/GroupedBarCli.java
bridges/GsaDiagCli.java
bridges/GxfFilterCli.java
bridges/GxfSortCli.java
bridges/HclustCli.java
bridges/HeatmapCli.java
bridges/HmmerSuiteCli.java
bridges/JgblocksCli.java
bridges/KeggEnrichCli.java
bridges/LayoutHeatmapCli.java
bridges/MCScanXCli.java
bridges/MCScanXFastCli.java
bridges/MSACli.java
bridges/MakeMotifCli.java
bridges/MarkerDesignCli.java
bridges/MarkerToolsCli.java
bridges/Mast2TabCli.java
bridges/MastCli.java
bridges/MastRunCli.java
bridges/Meme2TabCli.java
bridges/MemeCli.java
bridges/MemeRunCli.java
bridges/MgGxfCli.java
bridges/MicroSynCli.java
bridges/MirIdentifyCli.java
bridges/MotifCli.java
bridges/MotifPatternCli.java
bridges/MotifShiftCli.java
bridges/MountainPlotCli.java
bridges/MultiSuperHeatCli.java
bridges/NeedlemanWunschCli.java
bridges/PafGC.java
bridges/PafVizCli.java
bridges/PeakDistCli.java
bridges/Pep2CodonCli.java
bridges/PfamMotifCli.java
bridges/PhyloTreeCli.java
bridges/PileUpCli.java
bridges/PlantCAREResultClassifyCli.java
bridges/PubmedSearchCli.java
bridges/QpcrCli.java
bridges/QpcrDdctCli.java
bridges/QpcrProcCli.java
bridges/QuickGenomeDotCli.java
bridges/QuickProteinAnnoCli.java
bridges/QuickRunIQtreeCli.java
bridges/QuickTrimALCli.java
bridges/RNAplotCli.java
bridges/RegionBedToGFF3Cli.java
bridges/RegionDepthCli.java
bridges/SamBamCovCli.java
bridges/SeqConverterCli.java
bridges/SeqLenTrackCli.java
bridges/SeveralSpeciesCli.java
bridges/SimpleEnricherCli.java
bridges/SimpleHmmscanCli.java
bridges/SixFrameTranlaterCli.java
bridges/StructAnnoCompareCli.java
bridges/SubmitSMARTCli.java
bridges/SuperCircosCli.java
bridges/TableColManipCli.java
bridges/TableCollapseCli.java
bridges/TargetScoreCli.java
bridges/TauCalcCli.java
bridges/TaxonomyBatchCli.java
bridges/TreeCli.java
bridges/TreeRootingCli.java
bridges/TrimMSACli.java
bridges/UnrootedTreeCli.java
bridges/UpSetCli.java
bridges/Venn5Cli.java
bridges/Venn6Cli.java
bridges/ViolinCli.java
bridges/VisualizeCli.java
bridges/VizGFACli.java
bridges/javax/xml/bind/DatatypeConverter.java
bridges/jaxb-hack/javax/xml/bind/DatatypeConverter.java
config/config.sh
contracts/README.md
contracts/tools/amazingmeta.yaml
contracts/tools/annocompare.yaml
contracts/tools/autoMakeBlastDb.yaml
contracts/tools/bamMerge.yaml
contracts/tools/bamindex.yaml
contracts/tools/bamsort.yaml
contracts/tools/bamstate.yaml
contracts/tools/barplot.yaml
contracts/tools/barplotter.yaml
contracts/tools/batchReplace.yaml
contracts/tools/bed2gff3.yaml
contracts/tools/bestid.yaml
contracts/tools/blat.yaml
contracts/tools/calcRepeat.yaml
contracts/tools/careclassify.yaml
contracts/tools/cddmotif.yaml
contracts/tools/circlegene.yaml
contracts/tools/circos.yaml
contracts/tools/clearchar.yaml
contracts/tools/collinearRegion.yaml
contracts/tools/colorscheme.yaml
contracts/tools/conflictpaf.yaml
contracts/tools/ctgGroup.yaml
contracts/tools/cubeheatmap.yaml
contracts/tools/degramdom.yaml
contracts/tools/dehist.yaml
contracts/tools/distance.yaml
contracts/tools/dnDsCalculate.yaml
contracts/tools/dotplot.yaml
contracts/tools/draw.yaml
contracts/tools/dualsyn.yaml
contracts/tools/efpHeat.yaml
contracts/tools/exprCorr.yaml
contracts/tools/extractFasta.yaml
contracts/tools/fa2tab.yaml
contracts/tools/famerge.yaml
contracts/tools/fasplit.yaml
contracts/tools/fastaExtract.yaml
contracts/tools/fastaSubseq.yaml
contracts/tools/filterCScore.yaml
contracts/tools/fimo.yaml
contracts/tools/findblockdual.yaml
contracts/tools/findblockmultiple.yaml
contracts/tools/findhomolog.yaml
contracts/tools/findpath.yaml
contracts/tools/fqTrim.yaml
contracts/tools/fqfaConv.yaml
contracts/tools/gb2fa.yaml
contracts/tools/gbar.yaml
contracts/tools/gblocks.yaml
contracts/tools/gdensity.yaml
contracts/tools/gel.yaml
contracts/tools/genedensity.yaml
contracts/tools/genelocation.yaml
contracts/tools/genelocgff.yaml
contracts/tools/genestructure.yaml
contracts/tools/genomefilter.yaml
contracts/tools/getseqdb.yaml
contracts/tools/gfa.yaml
contracts/tools/gfa2fa.yaml
contracts/tools/goAnno.yaml
contracts/tools/goEnrich.yaml
contracts/tools/goParse.yaml
contracts/tools/golevel.yaml
contracts/tools/groupCol.yaml
contracts/tools/groupedbar.yaml
contracts/tools/gsea.yaml
contracts/tools/gxfAppend.yaml
contracts/tools/gxfAttr.yaml
contracts/tools/gxfFix.yaml
contracts/tools/gxfGenepos.yaml
contracts/tools/gxfIdAppender.yaml
contracts/tools/gxfMatch.yaml
contracts/tools/gxfOverlap.yaml
contracts/tools/gxfRecall.yaml
contracts/tools/gxfRegion.yaml
contracts/tools/gxfRename.yaml
contracts/tools/gxfRepGXF.yaml
contracts/tools/gxfRepIDs.yaml
contracts/tools/gxfSplit.yaml
contracts/tools/gxfStat.yaml
contracts/tools/hclust.yaml
contracts/tools/heatmap.yaml
contracts/tools/hicEnzyme.yaml
contracts/tools/hmmerSearch.yaml
contracts/tools/hmmsearch.yaml
contracts/tools/homoPhase.yaml
contracts/tools/iqtree.yaml
contracts/tools/kaks.yaml
contracts/tools/kallisto.yaml
contracts/tools/keggEnrich.yaml
contracts/tools/layoutheatmap.yaml
contracts/tools/levelGo.yaml
contracts/tools/logo.yaml
contracts/tools/longestorf.yaml
contracts/tools/makemotif.yaml
contracts/tools/mast.yaml
contracts/tools/mast2tab.yaml
contracts/tools/mastExtract.yaml
contracts/tools/mastrun.yaml
contracts/tools/mcscanx.yaml
contracts/tools/mcscanxd.yaml
contracts/tools/meme.yaml
contracts/tools/meme2tab.yaml
contracts/tools/memeViz.yaml
contracts/tools/memerun.yaml
contracts/tools/microgenome.yaml
contracts/tools/microsyn.yaml
contracts/tools/motif.yaml
contracts/tools/mountain.yaml
contracts/tools/mpattern.yaml
contracts/tools/msa.yaml
contracts/tools/msy.yaml
contracts/tools/multiEfp.yaml
contracts/tools/multisyn.yaml
contracts/tools/muscle.yaml
contracts/tools/newickRename.yaml
contracts/tools/notung.yaml
contracts/tools/nwAlign.yaml
contracts/tools/one-step.yaml
contracts/tools/onesteptree.yaml
contracts/tools/pafcomp.yaml
contracts/tools/pafref.yaml
contracts/tools/pafviz.yaml
contracts/tools/partitionconflict.yaml
contracts/tools/pca.yaml
contracts/tools/peakanno.yaml
contracts/tools/peakdist.yaml
contracts/tools/peaktss.yaml
contracts/tools/pep2codon.yaml
contracts/tools/pfammotif.yaml
contracts/tools/phylotree.yaml
contracts/tools/pileup.yaml
contracts/tools/plotrna.yaml
contracts/tools/preparespecies.yaml
contracts/tools/protparam.yaml
contracts/tools/protsim.yaml
contracts/tools/pubmed.yaml
contracts/tools/qdot.yaml
contracts/tools/qpcr.yaml
contracts/tools/qpcrExp.yaml
contracts/tools/quickAnno.yaml
contracts/tools/quickFamily.yaml
contracts/tools/recipBlast.yaml
contracts/tools/regionAnno.yaml
contracts/tools/rnaplot.yaml
contracts/tools/rooting.yaml
contracts/tools/sepChr.yaml
contracts/tools/seqfetch.yaml
contracts/tools/seqlentrack.yaml
contracts/tools/seqlogo.yaml
contracts/tools/seqpattern.yaml
contracts/tools/simplehmmscan.yaml
contracts/tools/sixframe.yaml
contracts/tools/smart.yaml
contracts/tools/sranum2info.yaml
contracts/tools/sraxml2tab.yaml
contracts/tools/sricher.yaml
contracts/tools/srr2ena.yaml
contracts/tools/stat-fasta.yaml
contracts/tools/statFasta.yaml
contracts/tools/structure.yaml
contracts/tools/subtree.yaml
contracts/tools/supercircos.yaml
contracts/tools/tab2fa.yaml
contracts/tools/tableAppend.yaml
contracts/tools/tableCast.yaml
contracts/tools/tableColSel.yaml
contracts/tools/tableColSelect.yaml
contracts/tools/tableCollapse.yaml
contracts/tools/tableMelt.yaml
contracts/tools/tableMerge.yaml
contracts/tools/tableSplit.yaml
contracts/tools/tableTranspose.yaml
contracts/tools/tableUniq.yaml
contracts/tools/tauIndex.yaml
contracts/tools/taxparse.yaml
contracts/tools/tfbsShift.yaml
contracts/tools/tpmCalc.yaml
contracts/tools/tree.yaml
contracts/tools/treeRooting.yaml
contracts/tools/trimal.yaml
contracts/tools/twoSeqBlast.yaml
contracts/tools/unrooted.yaml
contracts/tools/upset.yaml
contracts/tools/venn2.yaml
contracts/tools/venn3.yaml
contracts/tools/venn4.yaml
contracts/tools/venn5.yaml
contracts/tools/venn6.yaml
contracts/tools/violin.yaml
contracts/tools/virusRecomb.yaml
contracts/tools/visualizeblock.yaml
contracts/tools/volcano.yaml
contracts/tools/xml2blasttab.yaml
contracts/tools/xml2pairwise.yaml
tbtools_cli/__init__.py
tbtools_cli/artifact.py
tbtools_cli/auto_commands.py
tbtools_cli/cli.py
tbtools_cli/cli_load.py
tbtools_cli/cli_rpc.py
tbtools_cli/cli_tools_registry.py
tbtools_cli/cli_top.py
tbtools_cli/command_metadata.fingerprint.json
tbtools_cli/command_metadata.json
tbtools_cli/command_spec.py
tbtools_cli/compiler.py
tbtools_cli/config.example.toml
tbtools_cli/config.py
tbtools_cli/core.py
tbtools_cli/dependency.py
tbtools_cli/errors.py
tbtools_cli/executor.py
tbtools_cli/identity.py
tbtools_cli/mcp_server.py
tbtools_cli/meta_guard.py
tbtools_cli/presets.py
tbtools_cli/scenarios.py
tbtools_cli/source_scan.py
tbtools_cli/verification_report.json
tbtools_cli/workflow.py
tbtools_cli/runtime/__init__.py
tbtools_cli/runtime/env.py
tbtools_cli/runtime/i18n.py
tbtools_cli/runtime/java.py
tbtools_cli/runtime/validation.py