Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences.Kalignvu is an xml based alignment viewer that allows users to resize alignments and choose different colour schemes.
Mumsa is a tool for automatic assessment of alignment quality.
HMM-Kalign: a tool for generating sub-optimal HMM alignments.
Recent development of strategies using multiple sequence alignments (MSA) or profiles to detect remote homologies between proteins has led to a significant increase in the number of proteins whose structures can be generated by comparative modeling methods.
However, prediction of the optimal alignment between these highly divergent homologous proteins remains a difficult issue. We present a tool based on a generalized Viterbi algorithm that generates optimal and sub-optimal alignments between a sequence and a Hidden Markov Model. The tool is implemented as a new function within the HMMER package called hmmkalign.
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