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] |