# report filename

The report command outputs results. Although all analyses must be specified by their own commands, report directs the output of CAFE to filename (there is no need to add an extension to filename).

Here is a description of the output file (a tab-delimited summary of the results):

Tree: The current tree;
λ(s) and likelihood: The current λ values set by the lambda command; it can be either specified by the user (-t) or obtained by searching for the maximum likelihood value (-s). The likelihood of the data given the current λ value;
Average expansion: Mean number of genes gained or lost per family, where "minus" expansion is a net contraction;
Expansions and contractions: Total count of families that experienced expansions, contractions, or no change along each branch of the species tree;
List of family and description;
List of overall p-value for each family: The p-values are based on a Monte-Carlo re-sampling procedure. To determine the probability of a gene family with the observed sizes among taxa, CAFE will generate the expected distribution of family sizes under the stochastic birth-death model for the tree specified in the load command with the current λ value. Running the simulations uses the most machine resources and thus is the most time intensive step in CAFE. For each family in the data file, CAFE computes a probability (p-value) of observing the data given the average rate of gain and loss of genes. All else being equal, families with more variance in size are expected to have lower p-values.
List of branch-specific p-values for the significant families: The branch-specific p-values are obtained by the Viterbi method with the randomly generated likelihood distribution. This method calculates exact p-values for transitions between the parent and child family sizes for all branches of the phylogenetic tree. A low p-value indicates a rapidly evolving branch. This information is reported only for the families with an overall p-value less than the p-value cutoff set with the load command.
List of ancestral states for each family: Reports the maximum likelihood values of the ancestral number of genes at all inner nodes of all gene families.