Understanding ART output files

Each row in this table contains a tree ID and the ancestral pick for that tree. This file contains information about ALL trees, regardless if you use the '-t' argument. The command, 'calculate' generates this file.

This table shows information about trees, including log likelihood, probability, and cummulative probability. The rows are ordered by log-likelihood values, with the most likely trees first. Each row in the table has the following format:

[tree id] [probability] [log likelihood] [parenthetical tree]

This file is generated by the command, 'showtrees', and the set of output trees can be controlled with the '-t' argument.

This table contains the ancestral sequence for each tree, or the subset of trees specified by the '-t' argument, when 'findanc' is invoked. The rows are ordered numerically by tree IDs, in ascending order.

Each section of this file contains information about ancestral sequence-sites in each tree, or a subset of trees specified by the '-t' argument, when 'findanc' is invoked. The table is ordered by tree likelihood, with the most likely tree first.

map_ancestral_sequence contains the maximum a posteriori (MAP) sequence, along with probabilities of each site in the MAP sequence.