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3.5 Output Templates

An output template file consists of text with markup commands and placeholders for the program output. The text is copied into the final output. The backslash <\> character is used as an escape character, removing any special effect of the following character, so that it is treated as text. The markup commands currently have little effect, but may be useful in later versions if alternative output formats are supported. (e.g. tex, html, postscript, ...). The placeholders are replaced by the appropriate program output.

Markup commands start with the <<> character, and end with the next whitespace character. The end of the range of affected text is indicated with the <>> character.

The markup commands currently supported are:

This begins a comment – the text between this and the following <>> character is not included in the output.
This begins a table. Table columns are separated with the <&> character, and rows are separated with the <;> character.
This inserts another template file into the template. This allows partial templates to be reused in many output formats.
This has no effect. It is to allow for conditional markup commands. One condition can give one markup command, while another can give this noeffect command.

Placeholders begin with the <{> character and end with the <}> character. The first word of the placeholder is an expression, giving the value to be included. Currently only single variables are possible, but hopefully support for arithmetic expressions will be made available in later versions. The following variables are currently available:

A list of the variables selected. Useful if the --variableselect option is used.
The log likelihood at the current point.
Whether or not the algorithm converged.
The number of iterations of Newton-Raphson performed.
The number of the variable (usually in a table, where there will be a row for each variable.
The number of the variable within the original numbering from the input file. (This may be different from the variable number if only some variables are selected.)
Same as truevarnum cases
The coefficient of the variable. This is the parameter in the model provided to cold.
The exponential of the coefficient. This is the parameter used in some other models.
The modified t statistic for the variable. This can be used to test the hypothesis that the variable is non-zero.
The number of the branch.
The node above a branch.
The node below a branch.
The length of a branch.
The inferred tree. Currently only Newick format is supported.
The standard deviation of the estimated branch length (based on the observed information matrix).
The standard deviations of all branchlengths on a formatted tree.
The number of site classes.
The number of the current site class.
The mixing probability for the site class.
The number of the site.
The log-likelihood of the given site.
The posterior probabilities for the given site.
The hessian matrix at the estimate.
The inverse of the modified hessian matrix.

After the initial expression, various modifiers are allowed, affecting the way in which the output is formatted. The options vary, depending on the specific output. For example, there are options controlling the precision of numbers. For output that has only a discrete set of possible outcomes (such as @varnum, or @converge) the options can include a list of choices. This list is of the form value: followed by the text that should be displayed if the value matches, terminated with the <|> character.

Markup commands and placeholders can be nested using braces (<{> and <}>).