multiple sequence alignment using partition function posterior probabilities
Probalign uses partition function posterior probability estimates to
compute maximum expected accuracy multiple sequence alignments. It
performs statistically significantly better than the leading alignment
programs Probcons v1.1, MAFFT v5.851, and MUSCLE v3.6 on BAliBASE 3.0,
HOMSTRAD, and OXBENCH benchmarks. Probalign improvements are largest on
datasets containing N/C terminal extensions and on datasets with long
and heterogeneous length sequences. On heteregeneous length datasets
containing repeats Probalign alignment accuracy is 10% and 15% higher
than the other three methods when standard deviation of length is at
least 300 and 400.
