This directory contains a subset of alignments from BAliBASE version 3.0 (Thompson et al., 2005), which were used for the analysis by Herman et al. (2015). Further details for these alignments are available in the file bb3_release/README.

StatAlign v1.1 was run using the default settings for amino acids, with a burnin of $500,000$, and $2$ million sampling steps, taking alignment samples every $2000$ steps, thus producing $1000$ alignment samples for each test case. 

The program WeaveAlign was then used to compute minimum-risk summary alignments for each set of samples (see http://statalign.github.io/WeaveAlign for examples of how to run WeaveAlign).


References
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Thompson JD, Koehl P, Ripp R, Poch O (2005) "BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark." Proteins: Structure, Function, and Bioinformatics, 61:127–136.

Herman JL, Novák A, Lyngsø R, Szabó A, Miklós I and Hein J (2015) "Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs." BMC Bioinformatics (to appear)