fretree Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. 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 Phylip tree file: retree.dat Phylip tree output file [retree.treefile]: NEXT? (R . U W O T F D B N H J K L C + ? X Q) (? for Help): Q Do you want to write out the tree to a file? (Y or N): Y Enter R if the tree is to be rooted, OR enter U if the tree is to be unrooted: U Tree written to file "retree.treefile" 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 ** Go to the input files for this example Go to the output files for this example Command line arguments Interactive tree rearrangement Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-spp] integer [0] Number of species (Any integer value) [-intreefile] tree Phylip tree file [-outtreefile] outfile [*.fretree] Phylip tree output file Additional (Optional) qualifiers: -initialtree menu [Arbitary] Initial tree (Values: a (Arbitary); u (User); s (Specify)) -format menu [p] Format to write trees (Values: p (PHYLIP); n (NEXUS); x (XML)) -screenwidth integer [80] Width of terminal screen in characters (Any integer value) -vscreenwidth integer [80] Width of plotting area in characters (Any integer value) -screenlines integer [24] Number of lines on screen (Any integer value) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-outtreefile" associated qualifiers -odirectory3 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to 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 and exit. 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 dying program messages -version boolean Report version number and exit 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 ... tags. Each tree is included in tags ... . Each branch of the tree is enclosed in a pair of tags ... , 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: ... A tip of the tree is at the end of a branch (and hence that branch is enclosed in a pair of ... tags). Its name is enclosed by ... tags. Here is an XML tree: Mouse Bovine Gibbon Orang Gorilla Chimp Human 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. Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) 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. Comments None