Substory needs to be run after bppml. An example is provided in the Example folder.

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Meaning of the options to the program:

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Ancestral sequence reconstruction method (no other option for the moment):

asr.method=marginal

Report probabilities:

asr.probabilities=yes

If we want to sample from the posterior distribution of ancestral sequences, and get N=10 sequences per node, use these two options:

asr.sample=yes

How many samples should we use?

asr.sample.number=10

Shall we add extant sequences to output file?

output.nodes.add_extant = yes

Alignment information log file (site specific rates, probabilities, etc):

output.sites.file = $(DATA).sites.csv

Nodes information log file

output.nodes.file = $(DATA).nodes.csv

Write sequences:

output.sequence.file = $(DATA).ancestors.fasta output.sequence.format = Fasta

What type of substitutions do we want to keep track of?

map.type=All

Output all substitutions per branch (lines) and per type (columns)

output.mapping.file=substitutions.csv