confadd

Overview

confadd ("confidences addition") is a simple command line tool to calculate typed confidence values for a given evolutionary tree.Its input is typically one evolutionary tree which might or might not already have confidence values associated with its branches (the 'target') and a set (in the range of hundreds or more) of evolutionary trees (the 'evaluators') in which the frequency of splits represent confidences for the 'target'. The 'evaluators' are typically the result of a bootstrap re-sampling analysis or of a Bayesian method. 

Example:


confadd is implemented in Java as part of the forester libraries.

Input and Output

The minimal input is:

  • one or more evolutionary tree(s) (with possibly multiple, typed, support values already present, if described in phyloXML) in New Hampshire ('Newick'), Nexus, or phyloXML format [the 'target(s)']
  • a set (in the range of hundreds or more) of evolutionary trees in which the frequency of splits represent confidences for the 'target(s)', in New Hampshire ('Newick'), Nexus, or phyloXML format
  • a name for the type of confidence to be added (different from the types of confidences already present)

The output is:

  • for each 'target' tree: one tree with one additional type of confidence values added, written in phyloXML format

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Usage

java -Xmx2048m -cp path\to\forester.jar org.forester.application.confadd [options] <confidence type> <target tree file> <evaluators tree file> <outfile>

Options:
-s    : strict [default: non-strict]: all nodes between 'target' and 'evaluators' must match
-n=<d>: normalize to this value (e.g. 100 for most bootstrap analyses) [default: no normalization]
-f=<i>: first evaluator topology to use (0-based) [default: 0]
-l=<i>: last evaluator topology to use (0-based) [default: use all until final topology]

Example:
Adding bootstrap support from NJ trees based on a mafft alignment ('apaf1_mafft_nj.mlt', containing one-hundred topologies) to a ML tree based on a probcons alignment ('apaf1_probcons_raxml.xml'), labeling the support values to be added as 'bootstrap_mafft_nj', using the 'strict' option, and writing the result to 'apf1.xml':

"java -Xmx2048m -cp \soft\forester.jar org.forester.application.confadd -s bootstrap_mafft_nj apaf1_probcons_raxml.xml apaf1_mafft_nj.mlt apf1.xml"