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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]