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Cactus

  • Description

    a reference-free whole-genome multiple alignment program based upon notion of Cactus graphs.

  • Usage

    To list all executables provided by Cactus, run: $ biogrids-list cactus Copy to clipboard

  • Usage Notes

    Cactus provides the following executables:

    3EdgeTests blossom5 blossom_randGraph.py cPecanAlign cPecanEm cPecanLastz cPecanLastz_D cPecanLibTests cPecanModifyHmm cPecanRealign cactus cactus2hal.py cactus2hal-stitch.sh cactusAPITests cactus_addReferenceCoordinates cactus_analyseAssembly cactus_bar cactus_barTests cactus_batch_mergeChunks cactus_blast_chunkFlowerSequences cactus_blast_chunkSequences cactus_blast_convertCoordinates cactus_blast_sortAlignments cactus_caf cactus_calculateMappingQualities cactus_check cactus_convertAlignmentsToInternalNames cactus_coverage cactus_covered_intervals cactus_fastaGenerator cactus_fasta_fragments.py cactus_fasta_softmask_intervals.py cactus_fillAdjacencies cactus_filterSmallFastaSequences.py cactus_getReferenceSeq cactus_halGenerator cactus_halGeneratorTests cactus_makeAlphaNumericHeaders.py cactus_mirrorAndOrientAlignments cactus_normalisation cactus_phylogeny cactus_preprocess cactus_reference cactus_secondaryDatabase cactus_setup cactus_splitAlignmentOverlaps cactus_stripUniqueIDs cactus_workflow_convertAlignmentCoordinates cactus_workflow_extendFlowers cactus_workflow_flowerStats cactus_workflow_getFlowers dbTestScript findRegionsExclusivelyInGroup hal2assemblyHub.py hal2chain hal2fasta hal2maf hal2mafMP.py hal4dExtract hal4dExtractTest halAddToBranch halAlignedExtract halAlignmentDepth halApiTests halAppendCactusSubtree halAppendSubtree halBranchMutations halChainTests halCoverage halExtract halHdf5Tests halIndels halLiftover halLiftoverTests halLodExtract halLodInterpolate.py halMafTests halMaskExtract halRandGen halRemoveGenome halRenameGenomes halRenameSequences halReplaceGenome halSetMetadata halSingleCopyRegionsExtract halSnps halStats halSummarizeMutations halSynteny halTestGen halTreeMutations.py halTreeNIBackground.py halTreeNIConservation.py halTreeNITurnover.py halUpdateBranchLengths halValidate halWiggleLiftover halWriteNucleotides maf2hal matchGraph.py matchingAndOrderingTests mwmatching.py referenceTests sonLibTests sonLib_cigarTest sonLib_daemonize.py sonLib_fastaCTest sonLib_kvDatabaseTest stCafTests stPinchesAndCactiTests

  • Installation

    Use the following command to install this title with the CLI client: $ biogrids-cli install cactus Copy to clipboard Available operating systems: Linux 64

  • Primary Citation*

    J. Armstrong, G. Hickey, M. Diekhans, I. T. Fiddes, A. M. Novak, A. Deran, Q. Fang, D. Xie, S. Feng, J. Stiller, D. Genereux, J. Johnson, V. D. Marinescu, J. Alföldi, R. S. Harris, K. Lindblad-Toh, D. Haussler, E. Karlsson, E. D. Jarvis, G. Zhang, and B. Paten. 2020. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature. 587(7833): 246-251.


    • *Full citation information available through

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