The CONTRA (CONditional TRAining for Biosequence Analysis) Project is a collection of programs which apply discriminatively-trained probabilistic models (specifically conditional random fields and their variants) to a diverse array of sequence labeling problems in bioinformatics.
Currently, the CONTRA family includes:
|CONTRAlign, a protein sequence aligner|
|CONTRAfold, an RNA secondary structure folder|
|CONTRAST, a multiple sequence de novo gene predictor|