fdolmove |
Please help by correcting and extending the Wiki pages.
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.
% 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 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
Interactive Dollo or Polymorphism Parsimony Version: EMBOSS:6.4.0.0 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)) -thresh 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 |
Qualifier | Type | Description | Allowed values | Default | ||||||
---|---|---|---|---|---|---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||||||||
[-infile] (Parameter 1) |
discretestates | File containing data set | Discrete states file | |||||||
[-intreefile] (Parameter 2) |
tree | Phylip tree file (optional) | Phylogenetic tree | |||||||
Additional (Optional) qualifiers | ||||||||||
-weights | properties | Weights file | Property value(s) | |||||||
-ancfile | properties | Ancestral states file | Property value(s) | |||||||
-factorfile | properties | Factors file | Property value(s) | |||||||
-method | list | Parsimony method |
|
d | ||||||
-thresh | toggle | Use threshold parsimony | Toggle value Yes/No | No | ||||||
-threshold | float | Threshold value | Number 0.000 or more | 1 | ||||||
-initialtree | list | Initial tree |
|
Arbitary | ||||||
-screenwidth | integer | Width of terminal screen in characters | Any integer value | 80 | ||||||
-screenlines | integer | Number of lines on screen | Any integer value | 24 | ||||||
-outtreefile | outfile | Phylip tree output file (optional) | Output file | <*>.fdolmove | ||||||
Advanced (Unprompted) qualifiers | ||||||||||
(none) | ||||||||||
Associated qualifiers | ||||||||||
"-outtreefile" associated outfile qualifiers | ||||||||||
-odirectory | string | Output directory | Any string | |||||||
General qualifiers | ||||||||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||
-warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||
-error | boolean | Report errors | Boolean value Yes/No | Y | ||||||
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||
-die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
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.
5 6 Alpha 110110 Beta 110000 Gamma 100110 Delta 001001 Epsilon 001110 |
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.
(Epsilon,(Delta,(Gamma,(Beta,Alpha)))); |
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 | Estimates 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 | Distance matrix from restriction sites or fragments |
frestml | Restriction site maximum Likelihood method |
fseqboot | Bootstrapped sequences algorithm |
fseqbootall | Bootstrapped sequences algorithm |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
Converted (August 2004) to an EMBASSY program by the EMBOSS team.