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
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 |