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Table 2 List of programs and software packages utilized by SLFinder, including the version utilized in this paper and the basic tasks they carry out

From: SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

Program Version Tasks
Blast v2.6.0 Sequence searches against Transcriptome assemblies, Genome and Protein reference database.
cd-hit-est v4.7 Sequence clustering to simplify results and reduce runtimes
Jellifish v2.2.6 Kmer counts
MAFFT v7.307 Sequence Alignment
Seqkit v0.10.0 Basic sequence manipulation
trimAl v1.2rev59 Hook Variant generation by automatic trimming
Trinity v2.8.3 Hook assembly from Kmers
Weblogos v3.6.0 Sequence Logos generation to facilitate manual curation