fdolmove 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 Dollo or polymorphism parsimony Description Interactive construction of phylogenies from discrete character data with two states (0 and 1) using the Dollo or polymorphism parsimony criteria. Evaluates parsimony and compatibility criteria for those phylogenies and displays reconstructed states throughout the tree. This can be used to find parsimony or compatibility estimates by hand. Algorithm DOLMOVE is an interactive parsimony program which uses the Dollo and Polymorphism parsimony criteria. It is inspired on Wayne Maddison and David Maddison's marvellous program MacClade, which is written for Apple MacIntosh computers. DOLMOVE reads in a data set which is prepared in almost the same format as one for the Dollo and polymorhism parsimony program DOLLOP. It allows the user to choose an initial tree, and displays this tree on the screen. The user can look at different characters and the way their states are distributed on that tree, given the most parsimonious reconstruction of state changes for that particular tree. The user then can specify how the tree is to be rearraranged, rerooted or written out to a file. By looking at different rearrangements of the tree the user can manually search for the most parsimonious tree, and can get a feel for how different characters are affected by changes in the tree topology. This program is compatible with fewer computer systems than the other programs in PHYLIP. It can be adapted to PCDOS systems or to any system whose screen or terminals emulate DEC VT100 terminals (such as Telnet programs for logging in to remote computers over a TCP/IP network, VT100-compatible windows in the X windowing system, and any terminal compatible with ANSI standard terminals). For any other screen types, there is a generic option which does not make use of screen graphics characters to display the character states. This will be less effective, as the states will be less easy to see when displayed. Usage Here is a sample session with fdolmove % fdolmove Interactive Dollo or polymorphism parsimony Phylip character discrete states file: dolmove.dat Phylip tree file (optional): NEXT? (R # + - S . T U W O F 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 Interactive Dollo or polymorphism parsimony, version 3.69.650 5 species, 6 characters Computing steps needed for compatibility in sites ... (unrooted) 5.0 Steps 4 chars compatible Dollo ,-----------5:Epsilon --9 ! ,--------4:Delta `--8 ! ,-----3:Gamma `--7 ! ,--2:Beta `--6 `--1:Alpha Tree written to file "dolmove.treefile" Go to the input files for this example Go to the output files for this example Command line arguments Interactive Dollo or polymorphism parsimony Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-infile] discretestates File containing data set [-intreefile] tree Phylip tree file (optional) Additional (Optional) qualifiers (* if not always prompted): -weights properties Weights file -ancfile properties Ancestral states file -factorfile properties Factors file -method menu [d] Parsimony method (Values: d (Dollo); p (Polymorphism)) -dothreshold toggle [N] Use threshold parsimony * -threshold float [1] Threshold value (Number 0.000 or more) -initialtree menu [Arbitary] Initial tree (Values: a (Arbitary); u (User); s (Specify)) -screenwidth integer [80] Width of terminal screen in characters (Any integer value) -screenlines integer [24] Number of lines on screen (Any integer value) -outtreefile outfile [*.fdolmove] Phylip tree output file (optional) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-outtreefile" associated qualifiers -odirectory 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 fdolmove reads discrete character data with "?", "P", "B" states allowed. . (0,1) Discrete character data These programs are intended for the use of morphological systematists who are dealing with discrete characters, or by molecular evolutionists dealing with presence-absence data on restriction sites. One of the programs (PARS) allows multistate characters, with up to 8 states, plus the unknown state symbol "?". For the others, the characters are assumed to be coded into a series of (0,1) two-state characters. For most of the programs there are two other states possible, "P", which stands for the state of Polymorphism for both states (0 and 1), and "?", which stands for the state of ignorance: it is the state "unknown", or "does not apply". The state "P" can also be denoted by "B", for "both". There is a method invented by Sokal and Sneath (1963) for linear sequences of character states, and fully developed for branching sequences of character states by Kluge and Farris (1969) for recoding a multistate character into a series of two-state (0,1) characters. Suppose we had a character with four states whose character-state tree had the rooted form: 1 ---> 0 ---> 2 | | V 3 so that 1 is the ancestral state and 0, 2 and 3 derived states. We can represent this as three two-state characters: Old State New States --- ----- --- ------ 0 001 1 000 2 011 3 101 The three new states correspond to the three arrows in the above character state tree. Possession of one of the new states corresponds to whether or not the old state had that arrow in its ancestry. Thus the first new state corresponds to the bottommost arrow, which only state 3 has in its ancestry, the second state to the rightmost of the top arrows, and the third state to the leftmost top arrow. This coding will guarantee that the number of times that states arise on the tree (in programs MIX, MOVE, PENNY and BOOT) or the number of polymorphic states in a tree segment (in the Polymorphism option of DOLLOP, DOLMOVE, DOLPENNY and DOLBOOT) will correctly correspond to what would have been the case had our programs been able to take multistate characters into account. Although I have shown the above character state tree as rooted, the recoding method works equally well on unrooted multistate characters as long as the connections between the states are known and contain no loops. However, in the default option of programs DOLLOP, DOLMOVE, DOLPENNY and DOLBOOT the multistate recoding does not necessarily work properly, as it may lead the program to reconstruct nonexistent state combinations such as 010. An example of this problem is given in my paper on alternative phylogenetic methods (1979). If you have multistate character data where the states are connected in a branching "character state tree" you may want to do the binary recoding yourself. Thanks to Christopher Meacham, the package contains a program, FACTOR, which will do the recoding itself. For details see the documentation file for FACTOR. We now also have the program PARS, which can do parsimony for unordered character states. Input files for usage example File: dolmove.dat 5 6 Alpha 110110 Beta 110000 Gamma 100110 Delta 001001 Epsilon 001110 Output file format fdolmove output: If the A option is used, then the program will infer, for any character whose ancestral state is unknown ("?") whether the ancestral state 0 or 1 will give the fewest changes (according to the criterion in use). If these are tied, then it may not be possible for the program to infer the state in the internal nodes, and many of these will be shown as "?". If the A option is not used, then the program will assume 0 as the ancestral state. When reconstructing the placement of forward changes and reversions under the Dollo method, keep in mind that each polymorphic state in the input data will require one "last minute" reversion. This is included in the counts. Thus if we have both states 0 and 1 at a tip of the tree the program will assume that the lineage had state 1 up to the last minute, and then state 0 arose in that population by reversion, without loss of state 1. When DOLMOVE calculates the number of characters compatible with the tree, it will take the F option into account and count the multistate characters as units, counting a character as compatible with the tree only when all of the binary characters corresponding to it are compatible with the tree. Output files for usage example File: dolmove.treefile (Epsilon,(Delta,(Gamma,(Beta,Alpha)))); 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 distmat Create a distance matrix from a multiple sequence alignment ednacomp DNA compatibility algorithm ednadist Nucleic acid sequence distance matrix program ednainvar Nucleic acid sequence invariants method ednaml Phylogenies from nucleic acid maximum likelihood ednamlk Phylogenies from nucleic acid maximum likelihood with clock ednapars DNA parsimony algorithm ednapenny Penny algorithm for DNA eprotdist Protein distance algorithm eprotpars Protein parsimony algorithm erestml Restriction site maximum likelihood method eseqboot Bootstrapped sequences algorithm fdiscboot Bootstrapped discrete sites algorithm fdnacomp DNA compatibility algorithm fdnadist Nucleic acid sequence distance matrix program fdnainvar Nucleic acid sequence invariants method fdnaml Estimate nucleotide phylogeny by maximum likelihood fdnamlk Estimates nucleotide phylogeny by maximum likelihood fdnamove Interactive DNA parsimony fdnapars DNA parsimony algorithm fdnapenny Penny algorithm for DNA ffreqboot Bootstrapped genetic frequencies algorithm fproml Protein phylogeny by maximum likelihood fpromlk Protein phylogeny by maximum likelihood fprotdist Protein distance algorithm fprotpars Protein parsimony algorithm frestboot Bootstrapped restriction sites algorithm frestdist Calculate distance matrix from restriction sites or fragments frestml Restriction site maximum likelihood method fseqboot Bootstrapped sequences algorithm fseqbootall Bootstrapped sequences algorithm 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