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