Class support_transfer

Method Details

• main

  public static void main(String[] args)

  Transfers branch length values from one Phylogeny to another. It is mainly a "main method" for method "copyBranchLengthValuesFrom( Phylogeny )" of org.forester.phylogeny.Phylogeny, to be used in other (Perl) programs.

  Parameters:

  args - [0] Filename (String) for Phylogeny which has correct branch length values

  args - [1] String Filename (String) for Phylogeny to which the branch lengths of the first Phylogeny are to be copied, both Trees must only differ in their branch length values, i.e. topology and sequence names, etc. must be the same

  args - [2] String Filename (String) for outputfile

  args - [3] String [number of tree with correct bl to use in case treefile contains more than one, default 0]

• moveBranchLengthsToBootstrap

  public static final void moveBranchLengthsToBootstrap(Phylogeny p)

  Moves the values in the branch length field to the bootstrap field, for each PhylogenyNode of this Phylogeny. Converts a Phylogeny originating from a phylip treefile after bootstrapping and which therefore has its bootstrap values where the branch lenghts would be.

• transferSupportValues

  public static final void transferSupportValues(Phylogeny from, Phylogeny to)

  Modifies Phylogeny to with the support values from Phylogeny from. Important (but obvious): The topology of both trees needs to be the same. The method is not robust, and might produce wrong results if the internal topology differs or if the external node names are not unique.

  Parameters:

  from - the Phylogeny to copy the support values from

  to - the Phylogeny to copy the support values to