SP2ALIGN is a software and a web-server for pair-wise alignment of amino acid sequences by using weighted profiles of biochemical properties. This web-server finds an optimal global alignment of two amino acid sequences by utilizing weighted profiles of their biochemical properties instead of a single similarity matrix.
The TreeDet (Tree Determinant) Server is the first release of a system designed to integrate results from methods that predict functional sites in protein families. These methods take into account the relation between sequence conservation and evolutionary importance. TreeDet fully analyses the space of protein sequences in either user-uploaded or automatically generated multiple sequence alignments. The methods implemented in the server represent three main classes of methods for the detection of family-dependent conserved positions, a tree-based method, a correlation based method and a method that employs a principal component analyses coupled to a cluster algorithm.
CONTRAlign (CONditional TRAining for Protein Sequence Alignment)is an extensible and fully automatic parameter learning framework for protein pairwise sequence alignment based on pair conditional random fields. The CONTRAlign framework enables the development of feature-rich alignment models which generalize well to previously unseen sequences and avoid overfitting by controlling model complexity through regularization.