
                                  fretree 



Function

   Interactive tree rearrangement

Description

   Reads in a tree (with branch lengths if necessary) and allows you to
   reroot the tree, to flip branches, to change species names and branch
   lengths, and then write the result out. Can be used to convert between
   rooted and unrooted trees, and to write the tree into a preliminary
   version of a new XML tree file format which is under development and
   which is described in the RETREE documentation web page.

Algorithm

   RETREE is a tree editor. It reads in a tree, or allows the user to
   construct one, and displays this tree on the screen. The user then can
   specify how the tree is to be rearranged, rerooted or written out to a
   file.

   The input trees are in one file (with default file name intree), the
   output trees are written into another (outtree). The user can reroot,
   flip branches, change names of species, change or remove branch
   lengths, and move around to look at various parts of the tree if it is
   too large to fit on the screen. The trees can be multifurcating at any
   level, although the user is warned that many PHYLIP programs still
   cannot handle multifurcations above the root, or even at the root.

   A major use for this program will be to change rootedness of trees so
   that a rooted tree derived from one program can be fed in as an
   unrooted tree to another (you are asked about this when you give the
   command to write out the tree onto the tree output file). It will also
   be useful for specifying the length of a branch in a tree where you
   want a program like DNAML, DNAMLK, FITCH, or CONTML to hold that
   branch length constant (see the L suboption of the User Tree option in
   those programs. It will also be useful for changing the order of
   species for purely cosmetic reasons for DRAWGRAM and DRAWTREE,
   including using the Midpoint method of rooting the tree. It can also
   be used to write out a tree file in the Nexus format used by Paup and
   MacClade or in our XML tree file format.

   This program uses graphic characters that show the tree to best
   advantage on some computer systems. Its graphic characters will work
   best on MSDOS systems or MSDOS windows in Windows, and to any system
   whose screen or terminals emulate ANSI standard terminals such as old
   Digitial VT100 terminals, Telnet programs, or VT100-compatible windows
   in the X windowing system. For any other screen types, (such as
   Macintosh windows) there is a generic option which does not make use
   of screen graphics characters. The program will work well in those
   cases, but the tree it displays will look a bit uglier.

Usage

   Here is a sample session with fretree


% fretree 
Interactive tree rearrangement
Number of species [0]: 10
Input tree file: retree.dat


Reading tree file ...



                                      ,>>1:Human
                                   ,>22
                                ,>21  `>>2:Chimp
                                !  !
                             ,>20  `>>>>>3:Gorilla
                             !  !
                 ,>>>>>>>>>>19  `>>>>>>>>4:Orang
                 !           !
              ,>18           `>>>>>>>>>>>5:Gibbon
              !  !
              !  !              ,>>>>>>>>6:Barbary Ma
              !  `>>>>>>>>>>>>>23
              !                 !  ,>>>>>7:Crab-e. Ma
     ,>>>>>>>17                 `>24
     !        !                    !  ,>>8:Rhesus Mac
     !        !                    `>25
     !        !                       `>>9:Jpn Macaq
  ,>16        !
  !  !        `>>>>>>>>>>>>>>>>>>>>>>>>>10:Squir. Mon
  !  !
  !  !                                ,>11:Tarsier
** 7 lines below screen **

NEXT? (Options: R . U W O T F D B N H J K L C + ? X Q) (? for Help) Do you want
 to write out the tree to a file? (Y or N) Enter R if the tree is to be rooted
OR enter U if the tree is to be unrooted:
Tree written to file "retree.treefile"


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-spp]               integer    Number of species
  [-intreefile]        tree       (no help text) tree value

   Additional (Optional) qualifiers:
   -initialtree        menu       Initial tree
   -format             menu       Format to write trees
   -screenwidth        integer    Width of terminal screen in characters
   -vscreenwidth       integer    Width of plotting area in characters
   -screenlines        integer    Number of lines on screen

   Advanced (Unprompted) qualifiers:
   -outtreefile        outfile    Output file name

   Associated qualifiers:

   "-outtreefile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-spp]
   (Parameter 1) Number of species Any integer value 0
   [-intreefile]
   (Parameter 2) (no help text) tree value Phylogenetic tree
   Additional (Optional) qualifiers Allowed values Default
   -initialtree Initial tree
   a (Arbitary)
   u (User)
   s (Specify)
   Arbitary
   -format Format to write trees
   p (PHYLIP)
   n (NEXUS)
   x (XML)
   p
   -screenwidth Width of terminal screen in characters Any integer value
   80
   -vscreenwidth Width of plotting area in characters Any integer value
   80
   -screenlines Number of lines on screen Any integer value 24
   Advanced (Unprompted) qualifiers Allowed values Default
   -outtreefile Output file name Output file <sequence>.fretree

Input file format

   fretree reads any normal sequence USAs.

  Input files for usage example

  File: retree.dat

((((((((Human,Chimp),Gorilla),Orang),Gibbon),(Barbary_Ma,(Crab-e._Ma,
(Rhesus_Mac,Jpn_Macaq)))),Squir._Mon),((Tarsier,Lemur),Bovine)),Mouse);

Output file format

   The N (output file format) option allows the user to specify that the
   tree files that are written by the program will be in one of three
   formats:
    1. The PHYLIP default file format (the Newick standard) used by the
       programs in this package.
    2. The Nexus format defined by David Swofford and by Wayne Maddison
       and David Maddison for their programs PAUP and MacClade. A tree
       file written in Nexus format should be directly readable by those
       programs (They also have options to read a regular PHYLIP tree
       file as well).
    3. An XML tree file format which we have defined.

   The XML tree file format is fairly simple. The tree file, which may
   have multiple trees, is enclosed in a pair of <PHYLOGENIES> ...
   </PHYLOGENIES> tags. Each tree is included in tags <PHYLOGENY> ...
   </PHYLOGENY>. Each branch of the tree is enclosed in a pair of tags
   <CLADE> ... </CLADE>, which enclose the branch and all its
   descendants. If the branch has a length, this is given by the LENGTH
   attribute of the CLADE tag, so that the pair of tags looks like this:
   <CLADE LENGTH="0.09362"> ... </CLADE>

   A tip of the tree is at the end of a branch (and hence that branch is
   enclosed in a pair of <CLADE> ... </CLADE> tags). Its name is enclosed
   by <NAME> ... </NAME> tags. Here is an XML tree:

<phylogenies>
  <phylogeny>
    <clade>
      <clade length="0.87231"><name>Mouse</name></clade>
      <clade length="0.49807"><name>Bovine</name></clade>
      <clade length="0.39538">
        <clade length="0.25930"><name>Gibbon</name></clade>
        <clade length="0.10815">
          <clade length="0.24166"><name>Orang</name></clade>
          <clade length="0.04405">
            <clade length="0.12322"><name>Gorilla</name></clade>
            <clade length="0.06026">
              <clade length="0.13846"><name>Chimp</name></clade>
              <clade length="0.0857"><name>Human</name></clade>
            </clade>
          </clade>
        </clade>
      </clade>
    </clade>
  </phylogeny>
</phylogenies>

   The indentation is for readability but is not part of the XML tree
   standard, which ignores that kind of white space.

   What programs can read an XML tree? None right now, not even PHYLIP
   programs! But soon our lab's LAMARC package will have programs that
   can read an XML tree. XML is rapidly becoming the standard for
   representing and interchanging complex data -- it is time to have an
   XML tree standard. Certain extensions are obvious (to represent the
   bootstrap proportion for a branch, use BOOTP=0.83 in the CLADE tag,
   for example).

   There are other proposals for an XML tree standard. They have many
   similarities to this one, but are not identical to it. At the moment
   there is no mechanism in place for deciding between them other than
   seeing which get widely used. Here are links to other proposals:

   Taxonomic Markup Language http://www.albany.edu/~gilmr/pubxml/. and
   preprint at xml.coverpages.org/gilmour-TML.pdf published in the paper
   by Ron Gilmour (2000).
   Andrew Rambaut's BEAST XML phylogeny format See page 9 of PDF of BEAST
   manual at http://evolve.zoo.ox.ac.uk/beast/ An XML format for
   phylogenies is sketchly described there.
   treeml http://www.nomencurator.org/InfoVis2003/download/treeml.dtd
   (see also example: )
   http://www.cs.umd.edu/hcil/iv03contest/datasets/treeml-sample.xml
   Jean-Daniel Fekete's DTD for a tree XML file

   The W (screen and window Width) option specifies the width in
   characters of the area which the trees will be plotted to fit into.
   This is by default 80 characters so that they will fit on a normal
   width terminal. The actual width of the display on the terminal
   (normally 80 characters) will be regarded as a window displaying part
   of the tree. Thus you could set the "plotting area" to 132 characters,
   and inform the program that the screen width is 80 characters. Then
   the program will display only part of the tree at any one time.

  Output files for usage example

  File: retree.treefile

(((((((Human,Chimp),Gorilla),Orang),Gibbon),(Barbary_Ma,(Crab-e._Ma,
(Rhesus_Mac,Jpn_Macaq)))),Squir._Mon),((Tarsier,Lemur),Bovine),Mouse);

Data files

   None

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name                       Description
   fdrawgram    Plots a cladogram- or phenogram-like rooted tree diagram
   fdrawtree    Plots an unrooted tree diagram

Author(s)

   This program is an EMBOSS conversion of a program written by Joe
   Felsenstein as part of his PHYLIP package.

   Although we take every care to ensure that the results of the EMBOSS
   version are identical to those from the original package, we recommend
   that you check your inputs give the same results in both versions
   before publication.

   Please report all bugs in the EMBOSS version to the EMBOSS bug team,
   not to the original author.

History

   Written (2004) - Joe Felsenstein, University of Washington.

   Converted (August 2004) to an EMBASSY program by the EMBOSS team.

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
