Deprecated Apps Documentation
- soliver
- kkennedy
- mhelmke
Owned by soliver
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)