Probalign: 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% than the other three methods when standard deviation of length is at least 300 and 400.

• Java based Probalign 1.3 beta graphical user interface version now available for download here. Also contains standalone C++ source. Updates are posted frequently until stable version is released.
• Mac OS executable package for Probalign 1.3 beta graphical user interface version available here. To install, double click on the downloaded file and then double click on the application to start. Updates are posted frequently.
• Screenshots . Some of the features in 1.3 are
  • Average column posterior probability displayed in numbers and column colors
  • View columns with high average posterior probability
  • Save to pdf
• Older versions of Probalign available here.
• Please contact Usman Roshan (usman@cs.njit.edu) for support.

Citation: U. Roshan and D. R. Livesay, Probalign: Multiple sequence alignment using partition function posterior probabilities, Bioinformatics, In Press 2006, (PDF)

Data used in the paper:

• N/C extension simulated data. Includes all programs used for simulating the data as well as the simulated datasets.
• BAliBASE 2.0 repeat alignments. True alignments in FASTA format, core regions in upper case, and ambiguous ones in lower case. qscore program can be used for evaluating alignment accuracy
• BAliBASE 3.0, HOMSTRAD, and OXBENCH multiple sequence alignment benchmarks from the websites hosting the distributions.