Table 1. Bioinformatics applications and services included in Armadillo v1.1.

Bioinformatics tasks	Applications and services
Online Databank Access
National Center for Biotechnology Information (NCBI)	Access to database search and data downloads through the EUtils Web-servicesb
ENSEMBL-European Bioinformatics Institute (EBI)	Access to database search through EBI-Eye [58] and data downloads through dbFetch [14]
HUGO Gene Nomenclature Committee	Access to database search and downloads of human genes information
Multiple Sequence Alignment	BAli-phy [59], ClustalW [56], ClustalW2 [60], Kalign [61], Muscle [44], ProbCons [45]
Detection of Horizontal Gene Transfers	HGT Detection [51], PhyloNet – RIATA_HGT [52], LatTrans [53]
Phylogenetic Tree Inference	fastDNAml [62], DNAml-Erate [63], Garli [64], MrBayes [65], PhyML [46], PHYLIP package (11 applications included) [24], random tree generation program [25]
Phylogenetic Tree Visualization	PhyloWidget [40], Archaeopteryx [41], ScripTree [66]
Evolutionary Model Selection	jModelTest [55], ProtTest [57]
Selective Pressure Analysis	PAML v4.4 [6]
Local Alignment and Sequence Search with BLAST	BLAST (Local and Web at EBI and WTSI, and NCBI) [11]

See the Armadillo website for the complete list of included applications^a.

^aUp-to-date list of included applications is available at: http://adn.bioinfo.uqam.ca/armadillo/included.html.

^bNCBI EUtil is available at: http://www.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html.