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Discovery Environment Applications List

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Infernal Stage 3 (cmcalibrate) (archived)
Infernal Stage 4 (cmsearch) (archived)
LD_Plot (archived)
Linear regression in R (archived)
Lopper (archived)
Mermasker (archived)
MrBayes 3.2.1 MPI Basic App (archived)
Muscle Named Outputs (archived)
NCBI SRA Toolkit fastq-dump (archived)
Ornstein-Uhlenbeck models (archived)
PGDSpider convert data to different population genomics formats (archived)
Phylogenetics Muscle-PhyML (archived)
Picante (archived)
GLM_TASSEL 4.3.1 (archived)
QTLC workflow (archived)
QTLC Workflow2 (archived)
radtag demultiplex samples (archived)
Random Jungle 2.0.0 (archived)
Rename a file (archived)
RAxML - Nucleotides (archived)
RAxML - Proteins (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)
Select Markers to Keep v1 (archived)
Qxpak (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)
structure software (archived)
Structure v. 2.3.3 (archived)
Subset Reference Tree (archived)
Tallymer-mkindex (archived)
Tallymer-occratio (archived)
Tallymer-search (archived)
Tophat-SE (archived)
FastQC 0.10.1
tophat-2.1.1, tophat-2.1.0, and TopHat2-PE (archived)
TopHat Aligner for Single-End Illumina Reads (Custom Genome) (archived)
TopHat Aligner for Single-End Illumina Reads (archived)
TopHat Aligner for Paired-End Illumina Reads (archived)
TopHat Aligner for Paired-End Illumina Reads (Custom Genome) (archived)
TopHat2-SE (archived)
Tophat-SE-PE (archived)
Scythe-adapter-trimming (archived)
MetaGeneMark 2.26.0 (archived)

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Tophat-SE (archived)

Updated Aug 23, 2016

Tophat-SE (archived)

Aug 23, 2016

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