Table 1. Summary of Galaxy tools, wrappers for existing tools, and sample workflows discussed in this manuscript.

Some Galaxy tools are new pieces of software written specifically for use within Galaxy, others are wrappers allowing an existing tool to be used within Galaxy. Most of the tools wrapped are freely available under an open source license, however those marked ^⋆ are proprietary but free for academic use only, while ^† indicates free to download but with unspecified terms. Galaxy workflows are saved recipes or pipelines which automate running one or more Galaxy tools. See Materials and Methods for more details.

Galaxy Tool Shed URL, description	Type	References
http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
Standalone NCBI BLAST+ tools	Wrappers	Altschul et al. (1990);
		Camacho et al. (2009)
http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
BLAST datatype definitions (BLAST XML, databases)	Datatypes	Altschul et al. (1990);
		Camacho et al. (2009)
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
BLAST top hit descriptions	New tool
http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
Blast2GO for pipelines (b2g4pipe)	Wrapper†	Conesa et al. (2005);
		Götz et al. (2008)
http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
MIRA assembler	Wrapper	Chevreux, Wetter & Suhai (1999)
http://toolshed.g2.bx.psu.edu/view/bgruening/augustus
Augustus, for eukaryotic gene finding	Wrapper	Keller et al. (2011)
http://toolshed.g2.bx.psu.edu/view/bgruening/glimmer3
Glimmer3, for prokaryotic gene finding	Wrappers	Delcher et al. (2007)
http://toolshed.g2.bx.psu.edu/view/bgruening/repeat_masker
RepeatMasker, for screening DNA sequences	Wrapper	Smit, Hubley & Green (1996–2010)
http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan
InterProScan	Wrapper	Zdobnov & Apweiler (2001);
		Quevillon et al. (2005)
http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
SignalP, for signal peptide prediction	Wrapper⋆	Bendtsen et al. (2004)
TMHMM, for trans-membrane domain prediction	Wrapper⋆	Krogh et al. (2001)
PSORTb, for bacterial/archaeal proteins	Wrapper	Yu et al. (2010)
WoLF PSORT, for fungi/animal/plant proteins	Wrapper⋆	Horton et al. (2007)
Promoter, for eukaryotic PolII promoters	Wrapper⋆	Knudsen (1999)
Oomycete RXLR motifs	New Tool	Bhattacharjee et al. (2006);
		Win et al. (2007);
		Whisson et al. (2007)
http://toolshed.g2.bx.psu.edu/view/peterjc/predictnls
PredictNLS, predict nuclear localization sequence	Rewrite	Cokol, Nair & Rost (2000)
http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
NLStradamus, a nuclear localization sequence predictor	Wrapper	Nguyen Ba et al. (2009)
http://toolshed.g2.bx.psu.edu/view/peterjc/clinod
NoD, nucleolar localization sequence detector	Wrapper†	Scott et al. (2010); Scott, Troshin & Barton (2011)
http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
EffectiveT3, predicts bacterial type III secretion signals	Wrapper	Arnold et al. (2009); Jehl, Arnold & Rattei (2011)
http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
Venn Diagrams from (gene) identifier lists	New Tool
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
Filter sequences by (gene) identifier	New Tool
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
Select sequences by (gene) identifier	New Tool
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename
Rename identifiers in sequence files	New Tool
http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired
FASTQ deinterlacer for paired reads	New Tool
http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
Open reading frame (ORF) and crude coding sequence (CDS) prediction	New Tool
http://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_gene_calling_workflow
Glimmer gene calling with training-set	Workflow
http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
Secreted proteins using SignalP and THMHMM	Workflow	Cock & Pritchard (in press)
http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
Venn Diagram comparison of oomycete RXLR predictions	Workflow	Cock & Pritchard (in press)