The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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The apps in this list have been deprecated and are no longer available in the DE. If you need an app reinstated or have questions about a suitable replacement app, please contact



Page: FASTX nucleotide distribution (archived) Page: ERMINEJ (archived) Page: QTLC_Qstats (archived) Page: neighbor (archived) Page: PL (archived) Page: iPlantPhyloviewer (archived) Page: protdist (archived) Page: Find SNPs (archived) Page: Find Lambda and run PL (archived) Page: EMBOSS Diffseq (archived) Page: iPlantTASSEL (archived) Page: GFFRead Convert GFF to GTF (archived) Page: Standard File Format Testing and Conversion Tools (archived) Page: Random Jungle 2 (archived) Page: VCF to GFF3 documentation (archived) Page: Prodigal (archived) Page: AdjustPvalue 0.0.1 (archived) Page: CloudSTRUCTURE (archived) Page: Autodock Vina (archived) Page: 1000 Bulls GATK Genotyping 1.00 (archived) Page: ABySS Short Read Assembler (archived) Page: Agbase GOanna 1.02 (archived) Page: Agbase GOanna 2.03 (archived) Page: AgMIP QuadUI (archived) Page: 1000 Bulls GATK Genotyping (archived) Page: BEDTools annotateBed (archived) Page: BEDTools bedToBam (archived) Page: BEDTools closestBed (archived) Page: BEDTools clusterBed (archived) Page: BEDTools complementBed (archived) Page: BEDTools flankBed (archived) Page: BEDTools getOverlap (archived) Page: BEDTools groupBy (archived) Page: BEDTools mergeBed (archived) Page: BEDTools multiBamCov (archived) Page: BEDTools multiIntersectBed (archived) Page: BEDTools nucBed (archived) Page: BEDTools shuffleBed (archived) Page: BEDTools sortBed (archived) Page: BEDTools subtractBed (archived) Page: BEDTools windowBed (archived) Page: Bismark 0.7.4 (archived) Page: Bismark Genome Preparation 0.7.4 (archived) Page: Bismark Methylation Extractor 0.7.4 (archived) Page: Blastp-2.2.26 (archived) Page: BLASTX Contig Annotation (Stage 2) (archived) Page: Blat_the_most_basic_version (archived) Page: BWA 0.5.9 (archived) Page: BWA 0.59 (Paired-End Illumina Reads) (archived) Page: cd-hit 4.6.1 (archived) Page: CD-HIT-EST (archived) Page: CD-HIT-EST-2D-ISU-GROUP-D (archived) Page: Change Case (archived) Page: CONTRAST (archived) Page: Convert standard files for AntEpiSeeker (CvtAntEpiSeeker) (archived) Page: Convert standard files for Fast-LMM (CvtFastlmm) (archived) Page: Convert standard files to Random Jungle format (CvtRandomJungle) (archived) Page: Copy of Agbase GOanna 1.02 (archived) Page: Copy of Infernal Stage 4 (cmsearch) (archived) Page: Create BAM from SAM file (archived) Page: CuffCompare (archived) Page: Cuffdiff2a (archived) Page: cufflinks2gff3 (archived) Page: DACE (archived) Page: demultiplex samples (archived) Page: de novo construction genetic map (archived) Page: Detect text file types (archived) Page: Disparity through Time (archived) Page: DNAML (archived) Page: EBI Interproscan (Web Service) (archived) Page: EBI Interproscan 1.0.1 (Web Service) (archived) Page: eFP Batch Retrieve (archived) Page: EMBOSS backtranseq (archived) Page: EMBOSS Biosed (archived) Page: EMBOSS Charge (archived) Page: EMBOSS Checktrans (archived) Page: EMBOSS Codcmp (archived) Page: EMBOSS Coderet (archived) Page: EMBOSS Compseq (archived) Page: EMBOSS Cpgreport (archived) Page: EMBOSS Cutseq (archived) Page: EMBOSS Degapseq (archived) Page: EMBOSS Descseq (archived) Page: EMBOSS Dreg (archived) Page: EMBOSS Einverted (archived) Page: EMBOSS Equicktandem (archived) Page: EMBOSS Est2genome (archived) Page: EMBOSS Etandem (archived) Page: EMBOSS Extractfeat (archived) Page: EMBOSS Extractseq (archived) Page: EMBOSS Fuzznuc (archived) Page: EMBOSS Fuzzpro (archived) Page: EMBOSS Fuzztran (archived) Page: EMBOSS Geecee (archived) Page: EMBOSS Getorf (archived) Page: EMBOSS iep (archived) Page: EMBOSS Maskseq (archived) Page: EMBOSS Matcher (archived) Page: EMBOSS Megamerger (archived) Page: EMBOSS Msbar (archived) Page: EMBOSS Needle (archived) Page: EMBOSS Newcpgreport (archived) Page: EMBOSS Pepstats (archived) Page: EMBOSS Notseq (archived) Page: EMBOSS Prettyplot (archived) Page: EMBOSS Prettyseq (archived) Page: EMBOSS Revseq (archived) Page: EMBOSS Showfeat (archived) Page: EMBOSS Sigcleave (archived) Page: EMBOSS siRNA (archived) Page: EMBOSS Sixpack (archived) Page: EMBOSS Splitter (archived) Page: EMBOSS Supermatcher (archived) Page: EMBOSS Tcode (archived) Page: EMBOSS Textsearch (archived) Page: EMBOSS Tranalign (archived) Page: EMBOSS Trimest (archived) Page: EMBOSS Trimseq (archived) Page: EMBOSS Vectorstrip (archived) Page: EMBOSS Wordcount (archived) Page: EvoFold (archived) Page: FastLMM (archived) Page: FASTQ quality filter and trim (archived) Page: XYPlot 0.0.1 (archived) Page: TASSEL 4.3.0 (MLM) (archived) Page: Structure2Tassel 0.0.1 (archived) Page: NumericalTransform 0.0.1 (archived) Page: Filter Genotypes v1 (archived) Page: Find orthogroups by sequence similarity 0.1 (archived) Page: Find Unique Values (archived) Page: Forward_Regression-0.0.1 (archived) Page: GeneMania Query Runner (archived) Page: Generalized linear regression in R (archived) Page: GeneMania Query Runner 3.1 (archived) Page: GLMstructure (archived) Page: GLM Workflow (archived) Page: gluH2P (archived) Page: Homolog Resolution Service (archived) Page: Infernal Stage 1 (cmbuild) (archived) Page: Infernal Stage 2 (cmalign) (archived) Page: Infernal Stage 3 (cmcalibrate) (archived) Page: Infernal Stage 4 (cmsearch) (archived) Page: LD_Plot (archived) Page: Linear regression in R (archived) Page: Lopper (archived) Page: Mermasker (archived) Page: MrBayes 3.2.1 MPI Basic App (archived) Page: Muscle Named Outputs (archived) Page: NCBI SRA Toolkit fastq-dump (archived) Page: Ornstein-Uhlenbeck models (archived) Page: PGDSpider convert data to different population genomics formats (archived) Page: Phylogenetics Muscle-PhyML (archived) Page: Picante (archived) Page: GLM_TASSEL 4.3.1 (archived) Page: QTLC workflow (archived) Page: QTLC Workflow2 (archived) Page: radtag demultiplex samples (archived) Page: Random Jungle 2.0.0 (archived) Page: Rename a file (archived) Page: RAxML - Nucleotides (archived) Page: RAxML - Proteins (archived) Page: RNAfold (archived) Page: samtools_Sam_noheader_2Bam (archived) Page: SAMTOOLS-0.1.19 SAM-to-BAM-sans-header (archived) Page: SAMTOOLS-0.1.19 SORT BAM (archived) Page: SCARF (archived) Page: Select Markers to Keep v1 (archived) Page: Qxpak (archived) Page: SOAP 2.21 (archived) Page: SOAP2 Aligner for Paired-End Illumina Reads (archived) Page: SOAP2 Aligner for Single-End Illumina Reads (archived) Page: Soapdenovo-1.05 (archived) Page: SOAPdenovo-2 (archived) Page: SPA-1.0.0-Dev (archived) Page: structure software (archived) Page: Structure v. 2.3.3 (archived) Page: Subset Reference Tree (archived) Page: Tallymer-mkindex (archived) Page: Tallymer-occratio (archived) Page: Tallymer-search (archived) Page: Tophat-SE (archived) Page: FastQC 0.10.1 Page: tophat-2.1.1, tophat-2.1.0, and TopHat2-PE (archived) Page: TopHat Aligner for Single-End Illumina Reads (Custom Genome) (archived) Page: TopHat Aligner for Single-End Illumina Reads (archived) Page: TopHat Aligner for Paired-End Illumina Reads (archived) Page: TopHat Aligner for Paired-End Illumina Reads (Custom Genome) (archived) Page: TopHat2-SE (archived) Page: Tophat-SE-PE (archived) Page: Scythe-adapter-trimming (archived) Page: MetaGeneMark 2.26.0 (archived)