1 Installing foreseqs
Check the distributions for instructions.
2 Running foreseqs
Run `man foreseqs` or `foreseqs -h` for information about the
command line arguments. Example run:
$ foreseqs -i examples/alignment.4 -t examples/tree.4 -q examples/partitions.4
3 Branch length stealing
Stealing branch lengths averaging among partitions
$ foreseqs -i examples/alignment.4 -t examples/tree.4 -q examples/partitions.4 -b a
Stealing branch lengths estimating a partition scaler
$ foreseqs -i examples/alignment.4 -t examples/tree.4 -q examples/partitions.4 -b s
4 Sequence prediction algorithm
Predicting from Marginal Ancestral Probability Vectors (MAPV)
$ foreseqs -i examples/alignment.4 -t examples/tree.4 -q examples/partitions.4 -p m
Predicting from ancestral sequences
$ foreseqs -i examples/alignment.4 -t examples/tree.4 -q examples/partitions.4 -p s