fdnamove

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Function

Description

Algorithm

DNAMOVE is an interactive DNA parsimony program, inspired by Wayne Maddison and David and Wayne Maddison's marvellous program MacClade, which is written for Macintosh computers. DNAMOVE reads in a data set which is prepared in almost the same format as one for the DNA parsimony program DNAPARS. It allows the user to choose an initial tree, and displays this tree on the screen. The user can look at different sites and the way the nucleotide 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 sites are affected by changes in the tree topology.

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 Digital 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.

This program carries out unrooted parsimony (analogous to Wagner trees) (Eck and Dayhoff, 1966; Kluge and Farris, 1969) on DNA sequences. The method of Fitch (1971) is used to count the number of changes of base needed on a given tree.

The assumptions of this method are exactly analogous to those of MIX:

1. Each site evolves independently.
2. Different lineages evolve independently.
3. The probability of a base substitution at a given site is small over the lengths of time involved in a branch of the phylogeny.
4. The expected amounts of change in different branches of the phylogeny do not vary by so much that two changes in a high-rate branch are more probable than one change in a low-rate branch.
5. The expected amounts of change do not vary enough among sites that two changes in one site are more probable than one change in another.

That these are the assumptions of parsimony methods has been documented in a series of papers of mine: (1973a, 1978b, 1979, 1981b, 1983b, 1988b). For an opposing view arguing that the parsimony methods make no substantive assumptions such as these, see the papers by Farris (1983) and Sober (1983a, 1983b), but also read the exchange between Felsenstein and Sober (1986).

Change from an occupied site to a deletion is counted as one change. Reversion from a deletion to an occupied site is allowed and is also counted as one change.

Usage

% fdnamove Interactive DNA parsimony Input (aligned) nucleotide sequence set(s): dnamove.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 5 species, 13 sites Computing steps needed for compatibility in sites ... (unrooted) 19.0 Steps 11 sites compatible ,-----------5:Epsilon --9 ! ,--------4:Delta `--8 ! ,-----3:Gamma `--7 ! ,--2:Beta `--6 `--1:Alpha Tree written to file "dnamove.treefile"

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

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqsetall  (Aligned) nucleotide sequence set(s)
                                  filename and optional format, or reference
                                  (input USA)
  [-intreefile]        tree       Phylip tree file (optional)

   Additional (Optional) qualifiers (* if not always prompted):
   -weights            properties Weights file - ignore sites with weight zero
   -outgrno            integer    [0] Species number to use as outgroup
                                  (Integer 0 or more)
   -thresh             toggle     [N] Use threshold parsimony
*  -threshold          float      [1] Threshold value (Number 1.000 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    [*.fdnamove] Phylip tree output file
                                  (optional)

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-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. 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

Standard (Mandatory) qualifiers		Allowed values	Default
[-sequence] (Parameter 1)	(Aligned) nucleotide sequence set(s) filename and optional format, or reference (input USA)	Readable sets of sequences	Required
[-intreefile] (Parameter 2)	Phylip tree file (optional)	Phylogenetic tree
Additional (Optional) qualifiers		Allowed values	Default
-weights	Weights file - ignore sites with weight zero	Property value(s)
-outgrno	Species number to use as outgroup	Integer 0 or more	0
-thresh	Use threshold parsimony	Toggle value Yes/No	No
-threshold	Threshold value	Number 1.000 or more	1
-initialtree	Initial tree	a (Arbitary) u (User) s (Specify)	Arbitary
-screenwidth	Width of terminal screen in characters	Any integer value	80
-screenlines	Number of lines on screen	Any integer value	24
-outtreefile	Phylip tree output file (optional)	Output file	<*>.fdnamove
Advanced (Unprompted) qualifiers		Allowed values	Default
(none)

Input file format

Input files for usage example

File: dnamove.dat

   5   13
Alpha     AACGUGGCCA AAU
Beta      AAGGUCGCCA AAC
Gamma     CAUUUCGUCA CAA
Delta     GGUAUUUCGG CCU
Epsilon   GGGAUCUCGG CCC

Output file format

Output files for usage example

File: dnamove.treefile

(Epsilon,(Delta,(Gamma,(Beta,Alpha))));

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

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

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

Target users