TREEREEFINER is an efficient program for refining multiple alignment of genomic sequences based on a phylogenetic tree. It has demonstrated significant improvements in the accuracy of alignments generated by several popular aligners
Aswath Manohar , Serafim Batzoglou
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Proc IEEE Comput Syst Bioinform Conf. 2005:111-9.
TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree.
Manohar A, Batzoglou S.