BACKGROUND
Multiple sequences alignments play a key role in modern bioinformatics as becoming cornerstones of several types of investigations like protein family analysis, evolutionary inferred studies or comparative genomics. Depending on the study, the alignment is used to provide or host information. These information range from domain, motifs, protein secondary structure, hydrophobicity, phylogenetic tree, etc ... They are accessible through separated programs, and are generally stored in different files.

FINDINGS:
We present here ORDALIE [ORDered ALignment Information Explorer) 
We present here ORDALIE, an integrated workbench for manipulating and exploring the informational content of a multiple sequence alignment. ORDALIE is arranged around an internal SQLite database that allows storage and retreival of information. This allow also the storage of snapshots of the alignment corresponding to different studies (different clustering for instance) or different sequence alignment trials. Tools are also provided to decipher the informational content of the alignment.

CONCLUSION:
Although many software already exist to handle multiple sequence alignment or extract information,they are not linked entities and do not give an access to the information sphere cencerning a given alignment. Our platform ORDALIE gives a persistence of data decephered from alignment, and gives interconnecting tools allowing a broad variety of information mining for alignment exploitation.