Partial output of the Lineage-Specific Analysis with Minimum descendants set to 6. The complete output consists of both a table and a tree. The table has a row for each environment in each evaluated lineage/node. The nodes are named arbitrarily but can be viewed in the tree. Each evaluated node is colored based on its P-value in both the table and the tree. P-values < 0.001 are red, < .01 are yellow, < 0.05 are green, < .1 are blue and > 0.1 are gray. The table shows the observed and expected sequence counts for each environment for each evaluated node. The expected counts are what would be expected if the sequences were evenly distributed in the different lineages.
Lozupone et al. BMC Bioinformatics 2006 7:371 doi:10.1186/1471-2105-7-371