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

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.




Skip to end of metadata
Go to start of metadata

Viewing the User Manual for an App

Click the link to view the app's user manual. (You also can find the manuals for all current apps in the App Info for the app in the DE Apps list.)

 Looking for an app that you used but now isn't listed?

Search for an app in the search field below. Some apps have been deprecated and are no longer available in the list; the app manual may be available in the Deprecated Apps Documentation list.

To search for an app, enter the app name in the search box below.



Page: AAARF v 1.0.1 Page: add column to file Page: add column to file2 Page: Add GO to Blastp-uniprot output Page: Admixture Page: AgBase GOanna 2.1 Page: ALLMAPS Page: ALLMAPS merge Page: ALLMAPS path Page: AllpathsLG 44837 Page: AllpathsLG-small-genomes-44837 Page: Annotate transcripts Page: AntEpiSeeker 2.0 Page: appendUnclustered Page: Assembly Stats (assemblathon tool) Page: Assess Assembly vs whole genome Page: Bam to Counts (general) Page: BAM to Counts (named outputs) Page: BAM to SAM Page: bayesembler-1.2 Page: Bayesian BiClustering Page: bcftools view Page: BEAST2 on CyVerse UK Page: BEAST-2.1.3 Page: BEAST on CyVerse UK Page: BEDTools bamToBed Page: BEDTOOLS BAMtoFastq-2.19.1 Page: BEDTools coverageBed Page: BEDTools fastaFromBed Page: Bedtools Genome Coverage-BAM-2.19.1 Page: BEDTools genomeCoverageBed Page: BEDTools intersectBed Page: BEDTools maskFastaFromBed Page: BEDTools slopBed Page: Best Hit for Blat Output Page: Bismark Page: Bismark Genome Preparation Page: Bismark Methylation Extractor Page: Blast2Seqs Page: Blastn-2.2.26 Page: Blastn-2.6.0+ Page: Blastp-2.2.29 Page: Blastp-2.6.0+ Page: Blastp of a subset of uniprot Page: BLASTX (HPC) Page: BLAT_psl_to_SAM Page: Blat_with_BAM_output Page: blat_with_options Page: Blat (default) Page: Bowtie2-2.2.4 Bowtie2-Build indexer and aligner (HPC) Page: Bowtie2Build-2.2.4 indexer Page: Bowtie-2.2.1--Build-and-Map Page: Bowtie-Build Page: Bowtie--Build-and-Map Page: btrim Page: BuildICM-1.0.0-Dev Page: Bulk Blast 2 Sequences Page: BUSCO in the Discovery Environment Page: BUSCO-v2.0 in the Discovery Environment Page: BUSCO-v3.0 in the Discovery Environment Page: BWA 0.7.4 Divergent species Page: BWA 0.7.12 indexer aligner and mem (HPC) Page: BWA-0.7.4 non-model species Page: BWA_mem_longreads-0.7.15 Page: BWA Aligner for Paired-End Illumina Reads Page: BWA Aligner for Single-End Illumina Reads Page: BWA aln 0.7.4 Page: BWA index 0.7.4 Page: BWA mem 0.7.4 and 0.7.15 Page: bzip2 and bunzip2 Page: CACE Page: Calling SNPs INDELs with SAMtools BCFtools Page: Canberra Distance Page: CD-HIT-est 4.6.1 Page: CEGMA Page: CharaParser Learn Page: CharaParser Markup Page: Check covariance matrix file (CheckCvm) Page: Check standard GWAS files (CheckGwas) Page: Chromatra L Page: Chromatra T Page: Clean_fasta_header Page: ClustalW2 Page: clusterReport Page: CNVnator-0.3.3 Page: Compress a directory with GNU tar Page: Compress files with gzip Page: Compress selected files with GNU tar Page: Compute Contig Statistics Page: Concatenate 2 Files-workflow edition. Page: Concatenate Multiple Files Page: construction genetic map Page: Convert SAM-to-sorted-BAM Page: ConvertTraitID 0.0.1 Page: Copy with Scaffolding XML of DESeq2 (multifactorial pairwise comparisons) Page: Create BLAST database Page: Create BLAST database-2.6.0+ Page: create dir Page: Cuffcompare-2.2.1 Page: Cuffdiff Page: Cuffdiff2 Page: Cuffdiff2-16-way-max Page: Cuffdiff2 with JS option Page: CuffDiff 2.2.1a Page: Cufflinks Page: Cufflinks2 Page: Cufflinks_from_SAM-2.2.1 in DE Page: Cuffmerge Page: Cuffmerge2 Page: curl-7.45.0 Page: cutadapt Page: Cut Columns Page: De-interlace paired fasta Page: DeltaBLAST-2.2.29+ Page: de novo population genomics analysis Page: DESeq Page: DESeq2 Page: DESeq2 (multifactorial pairwise comparisons) Page: DNANJ Page: DNAPARS Page: dos2unix Page: Downsample reads Page: draw Venn diagrams Page: DREME Page: DynamicTrim Page: edgeR (multifactorial pairwise comparisons) in DE Page: edgeR with Fisher's Exact Test Page: EMBOSS Cusp Page: EMBOSS Seqret Page: Emboss transeq Page: Enhanced R Script Page: evolinc Page: Evolinc in the Discovery Environment Page: Extract First Lines From a File Page: Extract Last Lines From a File Page: FALCON (Small Genomes) 0.4.2 Page: FALCON-formatter Page: FASTA Minimum Size Filter Page: fastaRename Page: FaST-LMM-2.07 Page: FastLMM Result Plotter Page: FaST-LMM Results Plotter 2 Page: FaST-LMM Reults Plotter 2 Page: FASTQ_SHRINKER Page: FastQC Page: FastQC 0.10.1 (multi-file) Page: FastQC-0.11.5 (multi-file) Page: FastQC (demo) Page: fastqCombinePariedEnd Page: FastQC-plus 0.10.1 (multi-file) Page: Fastq-Join Page: Fastq-screen-0.4.4 Page: Fastq-screen-0.11.1 Page: FastTree2 Page: FastTree Dispatcher 2.1.4 Page: FASTX Barcode Splitter Page: FASTX Clipper Page: Fastx Collapser Page: FASTX Quality Filter Page: FASTX quality filter and trim Page: FASTX Quality Trimmer Page: FASTX Toolkit Page: FASTX Trimmer Page: Filter_CuffDiff_Results Page: Filter homozygous SNPs Page: filter pileup Page: Final filter Page: Final filter2 Page: Find Lines Matching a Regular Expression Page: Find SNPS - mpileup Page: flattenClusters 1.0 Page: Freebayes-0.9.20 Page: GapCloser 1.12 Page: GATK CombineGCVFs-3.2.2 Page: GATK GenotypeGVCFs-3.2.2 Page: GATK HaplotypeCaller-3.2.2 Page: GATK UnifiedGenotyper-3.2.2 Page: gbsAlign_BWA 0.5.9 Page: gbsFilter_TASSEL 3.0.133 Page: gbsMergeSNP_TASSEL 3.0.133 Page: gbsTags_TASSEL 3.0.133 Page: gbsTagsToSNP_TASSEL 3.0.133 Page: GBS Workflow Page: GBS Workflow with user genome Page: Generate detectability cartoons for syntenic features Page: GeneSeqer_5.0 Page: GeneSeqer-medium (Stampede) 5.0.0 Page: Genotype By Sequencing Page: Genotyping By Sequencing Workflow Page: GenSel Page: Gfold 1.1.1 Count Page: Gfold 1.1.1 Difference Expression Page: GLM Page: GMAP-7.23.15 Page: GNU awk Page: GNU grep 2.5.1 Page: GoSeq Page: GSNAP 07.23.15 Page: GSNAP 121212 Page: GWASSER Page: Head Page: Heterozygote BAM to Counts Page: Heterozygote BAM to Counts, v1.2 Page: Hisat2-Cuffcompare v1.0 Page: HISAT2-index-align Page: HTProcess_BAMstats-1.0 Page: HTProcess_CuffDiff-2.2.0 Page: HTProcess_Cufflinks-2.2.0 Page: HTProcess_Cufflinks-2.2.1 Page: HTProcess_Cuffmerge-1 Page: HTProcess_Cuffmerge-2.2.1 Page: HTProcess_fastqc-0.1 Page: HTProcess_fastqc-0.2 Page: HTProcess_Jellyfish-2.0.0 Page: HTProcess_Kmergenie-1.0 Page: HTProcess_Kmergenie-1.7016 Page: HTProcess_Tophat 2.0.13 (archived) Page: HTProcess_Tophat-2.0.11 (archived) Page: HTProcess_trimmomatic-0.33 Page: HTProcess_trimmomatic_0.32 Page: HTProcess-prepare_directories-and-run_fastqc-0.1 Page: HTProcess-prepare input directories 0.2 Page: HTProcess-prepare input directories-0.1 Page: HTProcess-Tophat-2.0.11 (archived) Page: HTProcess-Tophat-2.1.1 (archived) Page: HTSeq-count 0.5.4 Page: HTSeq-count-0.6.1 Page: HTSeq-with-BAM-input Page: IDBA-UD 1.1.2 Page: Identification of unique homozygous SNPs in mutant Page: IGVtools count Page: Index BAM file Page: Index BAM--get stats Page: Index fasta file (faidx) Page: InStruct Page: Interlace Paired FASTQ files Page: InterproScan 5.17.56 Page: InterProScan_Results_Function Page: IUTA-1.0 in the Discovery Environment Page: Join multiple tab-delimited files Page: Kallisto Page: KBase data upload Page: khmer filter-abund Page: khmer normalize by median Page: khmer strip-and-split-for-assembly Page: LASTAL-8.69 Page: LASTDB-8.69 Page: LD (Tassel4) Page: Linux stream editor Page: MACS Page: MAFFT 7.0.17 Page: Make new names for fasta sequences Page: maker2jbrowse Page: maker2zff Page: Mapping illumina seq data Part 1 Page: MaxBin 2.2 in the Discovery Environment Page: Megahit-1.0.6 Page: Merge-BAM-files Page: MergeG2P 0.0.2 Page: Merge SFF files-2.9 Page: MERRA-AS instM_3d_ana_Np (Analyzed State, Meteorology Instantaneous Monthly) Page: MERRA-AS tavg1_2d_lnd_Nx (Land related surface quantities) Page: MetaGeneAnnotator-1.0.0 Page: MetaGeneMark 2.26.0 Page: MetaGeneMark GFF to IGB Page: MetaPhyler-SR 0.115 Page: MetaQUAST-4.0 (denovo based) in DE Page: MetaQUAST-4.0 (reference based) in DE Page: MetaQUAST-4.3 (denovo based) in DE Page: MetaQUAST-4.3 (reference based) in DE Page: Mikado Page: miRanda Page: MLM 4.3.13 Page: MLM (Tassel4) Page: MLMM 0.0.2 Page: MLM Workflow Page: Modify_GFF_coordinates Page: Molecular Dating with Penalized Likelihood Page: mpileup Page: MrBayes_mpi_basic-3.2.3 Page: MrBayes on CyVerse UK Page: MUSCLE Page: MUSCLE-3.8.31 on Stampede Page: Mutant Identification 1 Page: mutant interval identification Page: Nanopolish-eventalign-0.7.1 Page: Nanopolish-extract-0.8.1 Page: Nanopolish-index-0.8.1 Page: NCBI GenBank Import Page: NCBI SRA Import Page: NCBI SRA Import 1.2 Page: NCBI SRA Submission - BioProject Creation Page: NCBI SRA Submission - BioProject Update Page: NCBI SRA Submission Report Retrieval Page: NCBI SRA Toolkit fastq-dump 2.1.9 Page: NCBI SRA Toolkit fastq-dump 2.3.4 Page: NCBI SRA Toolkit fastq-dump 2.8.1 Page: NCBI SRA to Solid Format (abi-dump) Page: Newbler Page: Newbler 2.6.0 Page: Ninja Page: non-unique filter Page: Normalize By Median Page: NPUTE-0.0.1 Page: NumericalTransform 4.3.14 Page: Numeric Evaluation of a Data Column Page: Oases 0.2.08 Page: Ontologizer Page: OrthoMCL v1.4 Page: PAGE Page: PAML Page: ParaAT 2.0 Page: parallel-fastq-dump - 0.6.1 Page: parseBlastBpo Page: Parse Blast Report Page: PcPipe 1.0.0 Page: Peak Ranger Page: PepMOD Page: PGDSpider tool for data conversion Page: Photometry-pipeline-v1.0 Page: PhyML Page: Picard-MarkDuplicates-2.7.1 in the Discovery Environment Page: Picard Preprocess-1.98 Page: pigz-2.3.4 (Compress multiple files with gzip parallely) Page: PK Unzip Page: Platypus- Page: PLINK Page: PLINK 2 AntEpiSeeker Conversion Page: PLINK Conversion Page: Polymarker Page: population genomics analysis flow Page: Pre-Process Reads Page: Principal Component Analysis Page: Prinseq-Graph-noPCA evaluate reads Page: Prinseq-lite Page: Prodigal Page: ProgressiveMauve Page: PROML Page: PROTNJ Page: PROTPARS Page: QIIME-1.9.1 in Discovery Environment Page: QTL Cartographer Page: QTL simulation workflow Page: QUAST (3.2 and 4.0) in the Discovery Environment Page: queryOrthoMCL 1.0 Page: Rascaf V1.0.2 in Discovery Environment Page: RAxML-7.3.0 Page: RAxML-8.2.3_small_and_medium Page: RAxML on CyVerse UK Page: Ray-2.3.1 Page: remove duplicates Page: Rename contigs 2.0 Page: rePair-Fix Read Pairing Page: rnaQUAST 1.2.0 (reference based) using DE Page: rnaQUAST_1.2.0 (de novo based) Page: RSEM 1.2.12 Page: RSEM-Prepare-Reference 1.2.19 Page: Sabre-barcode-demultiplexing Page: Sailfish_align_quant-0.9.2 Page: salmon-index-quant-0.8.1 Page: SAM_to_Sorted_BAM-0.1.9 Page: SAMTOOLS-0.1.19 mpileup raw-vcf-out Page: SAMTOOLS-0.1.19 mpileup variant pipeline Page: SAMTOOLS-0.1.19 VCF-Utilities varFilter Page: Samtools_mapping_stats-1.0 Page: Samtools faidx (fasta indexer) Page: SAMtools index BAM file Page: SAMTools mpileup Page: SAMTools SAM to sorted BAM Page: SAM to sorted BAMv2 Page: Scythe-0.991 using DE Page: Select contigs Page: seqtk_seq-1.0.76 Page: SequenceLogo Page: Sff2Fastq Page: Sickle-quality-based-trimming version 1.0 Page: SKAT Page: Snap, gene prediction Page: Snap-gene prediction-112913 Page: snp_ase Page: SNP calling illumina seq data Part 2 Page: Soapdenovo Page: Soapdenovo 2.04 Page: Soapdenovo-Trans 1.0 Page: Soapdenovo-trans-small-1.0.4 Page: Sort a File On A Column Page: Sort Bam Page: Sort File On 2 columns Page: SPAdes-3.8.0 Page: Spladder-1.0.0 Page: Split FASTA file Page: SRA-Import-0.1.0 Page: Stampy-build-and-map Page: STAR_2.4.0.1 Page: STAR_2.4.0.1_GenerateGenomeIndex Page: Star-index-align_2.5.3.a Page: StringTie1.3.3 Page: StringTie-1.3.3_merge Page: Structure2Tassel Page: Suffixerator Page: Syntenic_Feature_Detector Page: taco-0.7.0 Page: Tassel3 Conversion Page: Tassel4 Conversion Page: tbl2asn (gapped)-22.9 using DE Page: tbl2asn (gapped)-25.3 using DE Page: tbl2asn (ungapped)-22.9 using DE Page: tbl2asn (ungapped)-25.3 using DE Page: TIES baseline 1 - averaging Page: TIES baseline 2 - line fitting Page: TIES basic complete run (rev A) Page: TIES step 1 - parse input CSV data Page: TIES step 2 - training full LSS model Page: tophat2gff3 Page: Transcript decoder 1.0 Page: Transcript decoder 2.0 Page: TreeView Page: trim_galore-0.4.1 using DE Page: Trimmomatic-programmable-0.33 Page: Trimmomatic-programmable-0.36 Page: Trinity-64GB-2.1.1 Page: Trinity normalize by k-mer coverage r11.10.13 Page: Trinity r2013-08-14a Page: Trinity r2013-11-10 Page: Tuxedo suite PE up to 4 conditions Page: Uncompress files with gunzip Page: Uncompress with gunzip Page: Uncompress with tar Page: UNEAK Page: unique filter Page: unpigz-2.3.4 (Uncompress multiple files with ungzip parallely) Page: Validate Page: Variable Region Identifier and Remover Page: VarScan-2.3.6 SNP caller Page: VCF to GFF3 Page: varFilter Page: vContact_0.1.49 and vContact-PCs Page: Velvetg-1.2.07 Page: Velvetg-1.2.10 Page: Velvetg-1.2.075 Page: Velvetg-1.2.075-assembly-step2 Page: Velveth-1.2.07 Page: Velveth-1.2.10 Page: Viral Contaimination Detection 1.0 Page: VirSorter 1.0.1 Page: VIRSorter 1.0.2 Page: Weka 3.7.11 Page: Word Count Page: XYPlot 0.0.2