fdnamove |
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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:
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.
% 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
Interactive DNA parsimony Version: EMBOSS:6.4.0.0 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 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 | ||||||||||
[-sequence] (Parameter 1) |
seqsetall | (Aligned) nucleotide sequence set(s) filename and optional format, or reference (input USA) | Readable sets of sequences | Required | ||||||
[-intreefile] (Parameter 2) |
tree | Phylip tree file (optional) | Phylogenetic tree | |||||||
Additional (Optional) qualifiers | ||||||||||
-weights | properties | Weights file - ignore sites with weight zero | Property value(s) | |||||||
-outgrno | integer | Species number to use as outgroup | Integer 0 or more | 0 | ||||||
-thresh | toggle | Use threshold parsimony | Toggle value Yes/No | No | ||||||
-threshold | float | Threshold value | Number 1.000 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 | <*>.fdnamove | ||||||
Advanced (Unprompted) qualifiers | ||||||||||
(none) | ||||||||||
Associated qualifiers | ||||||||||
"-sequence" associated seqsetall qualifiers | ||||||||||
-sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 | ||||||
-send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 | ||||||
-sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||
-sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||
-snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||
-sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||
-slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N | ||||||
-supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N | ||||||
-sformat1 -sformat_sequence |
string | Input sequence format | Any string | |||||||
-sdbname1 -sdbname_sequence |
string | Database name | Any string | |||||||
-sid1 -sid_sequence |
string | Entryname | Any string | |||||||
-ufo1 -ufo_sequence |
string | UFO features | Any string | |||||||
-fformat1 -fformat_sequence |
string | Features format | Any string | |||||||
-fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |||||||
"-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 |
5 13 Alpha AACGUGGCCA AAU Beta AAGGUCGCCA AAC Gamma CAUUUCGUCA CAA Delta GGUAUUUCGG CCU Epsilon GGGAUCUCGG CCC |
(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 |
fdnapars | DNA parsimony algorithm |
fdnapenny | Penny algorithm for DNA |
fdolmove | Interactive Dollo or Polymorphism Parsimony |
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.