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jujubix / simulfold

simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework
http://www.e-rna.org/simulfold/
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javac -O *.java

java SimulFold initial_alignment_file initial_tree_file [-T] [-A] [-S]

The alignment file must be in fasta-format, the tree must be in rooted tree newick format, and white spaces are not allowed. The headers in the fasta file must match the labels in the newick file.

The optional -T flag will allow tree movements in MCMC, the optional -A flag will allow alignment movements in MCMC, the optional -S flag will allow structure movements in the MCMC.