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Table 1 Bioinformatics software or packages incorporated on STINGRAY workflow

From: STINGRAY: system for integrated genomic resources and analysis

Software/packages Workflow function Ref.
MIRA Assembly [10]
Velvet Assembly [11]
Phred Reads quality match [12]
Crossmatch Vector mask [12]
RepeatMasker Repeat sequence mask [13]
CAP3 Sequences clusterization [14]
Glimmer3 Prokaryotic gene prediction [15]
GlimmerHMM Eukaryotic gene prediction [16]
Geecee G + C content calculation [17]
Cusp Codon usage calculation [17]
tRNA-scan tRNA search [18]
BLAST Similarity search [19]
Rps-BLAST Conserved domain search [19]
Psi-BLAST Similarity search [19]
Signalp Signal peptide cleavage sites prediction [20]
Wolf-Psort Protein localization [21]
MAFFT Multiple sequence alignment construction [22]
ProbCons Multiple sequence alignment construction [23]
WebLogo Alignment logos generation [24]
Ancescon Ancestor sequence prediction [25]
Phylip Phylogenetic tree construction [26]
Weighbor Phylogenetic tree construction [27]
ModelGenerator Evolutionary model search [28]