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FastME

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Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle.

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Running FastME

FastME first builds an initial tree, using either OLS_GME, balanced_GME, NJ or BIONJ algorithms, and then improves this tree by tree swapping, using either OLS_NNI or balanced_NNI algorithms. OLS_GME and OLS_NNI optimize the ordinary least-squares (OLS) version of the minimum-evolution principle, while balanced_GME and balanced_NNI optimize the balanced version. NJ also optimizes the balanced version (Gascuel & Steel 2006). All simulations indicate that the balanced version is much more appropriate. But the initial tree has not much influence on the final tree that is obtained after tree swapping. The default options are balanced_GME and balanced_NNI, but OLS_GME, NJ and BIONJ can be used to build the starting tree as well. In all cases balanced_NNI has to be used, at least when building phylogenies using evolutionary distances estimated from sequences. More explanations about the algorithms and their range of use are given in the papers above. Distance matrices must be in PHYLIP square format. When the input file contains several matrices given one after the other, as obtained when combining SEQBOOT and DNADIST or PROTDIST to perform a bootstrap analysis, FastME returns the same number of trees, written one after the other in the output file; this file may be given to CONSENSE to obtain the bootstrap tree.

You can use FastME with PHYLIP-like interface or with the command line.

PHYLIP-like interface options

The interface always suggests the more relevant parameters.

• M to specify the method for building initial tree: (b)alanced_GME (default), (O)LS_GME, (N)J, B(I)ONJ, (U)NJ or user defined topology file.
• D to set the number of datasets (default = 1).
• N to set the type of tree swapping (default is balanced_NNI).
• W to select the branch lengths assigned to the topology: (b)alanced (default) or (O)LS.
  This option is available only when not doing NNI (N option set to 'none').
  In this case FastME estimates the branch lengths of the topology, according to one of the two approaches.
  W (none) is available only with NJ, BIONJ or UNJ tree building method. In this case, FastME just returns the tree.
• S to compute SPR postprocessing.
• T to compute TBR postprocessing.

Command line options

• -a, --append
  Use this option to append results to existing output files (if any).
  By default output files will be overwritten.
• -d datasets, --datasets=datasets
  Use this option to indicate the number of datasets in your input data file.
  The default number of datasets is 1.
• -h, --help
  Display this usage.
• -i input data file, --input_data=input data file
  The input data file contains distance matrix(ces).
• -I output information file, --output_info=output information file
  Use this option if you want fastme to write information about its execution in the output information file.
• -m method, --method=method
  fastme computes a tree using a distance algorithm.
  You may choose this method from: (b)alanced_GME (default), (O)LS_GME, B(I)ONJ, (N)J or (U)NJ.
• -n NNI, --NNI=NNI
  This option sets the type of tree swapping (NNI)
  You may choose the NNI type from: (b)alanced_NNI (default), (O)LS_NNI or (n)one.
• -o output tree file, --output_tree=output tree file
  fastme will write the infered tree into the output tree file.
• -s, --SPR
  Use this option to do SPR postprocessing.
• -S scoring matrix file, --input_scoring=scoring matrix file
  Use this option if you want fastme to compute distance from alignment using data in the scoring matrix file.
• -t, --TBR
  Use this option to do TBR postprocessing.
• -T input tree file, --input_topology=input tree file
  fastme may use an existing topology available in the input tree file which corresponds to the input dataset.
• -v, --verbose
  Use this option to turn fastme in verbose mode.
• -w branch, --branch_length=branch
  Use this option to indicate the branch length to assign to the tree.
  You may choose the branch length from: (b)alanced (default), (O)LS or (n)one. (n)one is only available with BIONJ, NJ or UNJ.
  Only helpful when not doing NNI.

For example, assuming that the datatest file (downloaded from this web page, see above) is within /home/ directory, the command line:
fastme –i /home/datatest.txt –d 3
will construct 3 trees and write them (Newick format) into the outputtree file (/home/dataset.txt.tree.txt). A second file (/home/dataset.txt.stat.txt) is created, containing options selected by the user and some statistics (estimated tree length and number of NNIs performed). When something is wrong (e.g. the input file name), you will get the list of all options.

Webmaster: Vincent Lefort, LIRMM.