simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework
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Alignment.class
AlignmentColumn.class
AlignmentProposal.class
COPYRIGHT
MCMC.class
MCMC.java
README
SimulFold.class
SimulFold.java
SingleStranded.class
Tree.class
TreeNode.class

README

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.