|   | fdnapars | 
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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, 1988), 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. Note that this in effect assumes that a deletion N bases long is N separate events.
Dnapars can handle both bifurcating and multifurcating trees. In doing its search for most parsimonious trees, it adds species not only by creating new forks in the middle of existing branches, but it also tries putting them at the end of new branches which are added to existing forks. Thus it searches among both bifurcating and multifurcating trees. If a branch in a tree does not have any characters which might change in that branch in the most parsimonious tree, it does not save that tree. Thus in any tree that results, a branch exists only if some character has a most parsimonious reconstruction that would involve change in that branch. It also saves a number of trees tied for best (you can alter the
number it saves using the V option in the menu). When rearranging trees, it tries rearrangements of all of the saved trees. This makes the algorithm slower than earlier versions of Dnapars.
The input data is standard. The first line of the input file contains the number of species and the number of sites.
Next come the species data. Each sequence starts on a new line, has a ten-character species name that must be blank-filled to be of that length, followed immediately by the species data in the one-letter code. The sequences must either be in the "interleaved" or "sequential" formats described in the Molecular Sequence Programs document. The I option selects between them. The sequences can have internal blanks in the sequence but there must be no extra blanks at the end of the terminated line. Note that a blank is not a valid symbol for a deletion.
| % fdnapars DNA parsimony algorithm Input (aligned) nucleotide sequence set(s): dnapars.dat Phylip tree file (optional): Phylip dnapars program output file [dnapars.fdnapars]: Adding species: 1. Alpha 2. Beta 3. Gamma 4. Delta 5. Epsilon Doing global rearrangements on the first of the trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "dnapars.fdnapars" Tree also written onto file "dnapars.treefile" Done. | 
Go to the input files for this example
Go to the output files for this example
| 
DNA parsimony algorithm
Version: EMBOSS:6.6.0.0
   Standard (Mandatory) qualifiers:
  [-sequence]          seqsetall  File containing one or more sequence
                                  alignments
  [-intreefile]        tree       Phylip tree file (optional)
  [-outfile]           outfile    [*.fdnapars] Phylip dnapars program output
                                  file
   Additional (Optional) qualifiers (* if not always prompted):
   -weights            properties Weights file
   -maxtrees           integer    [10000] Number of trees to save (Integer
                                  from 1 to 1000000)
*  -[no]thorough       toggle     [Y] More thorough search
*  -[no]rearrange      boolean    [Y] Rearrange on just one best tree
   -transversion       boolean    [N] Use transversion parsimony
*  -njumble            integer    [0] Number of times to randomise (Integer 0
                                  or more)
*  -seed               integer    [1] Random number seed between 1 and 32767
                                  (must be odd) (Integer from 1 to 32767)
   -outgrno            integer    [0] Species number to use as outgroup
                                  (Integer 0 or more)
   -dothreshold        toggle     [N] Use threshold parsimony
*  -threshold          float      [1.0] Threshold value (Number 1.000 or more)
   -[no]trout          toggle     [Y] Write out trees to tree file
*  -outtreefile        outfile    [*.fdnapars] Phylip tree output file
                                  (optional)
   -printdata          boolean    [N] Print data at start of run
   -[no]progress       boolean    [Y] Print indications of progress of run
   -stepbox            boolean    [N] Print out steps in each site
   -ancseq             boolean    [N] Print sequences at all nodes of tree
   -[no]treeprint      boolean    [Y] Print out tree
*  -[no]dotdiff        boolean    [Y] Use dot differencing to display results
   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name
   "-outfile" associated qualifiers
   -odirectory3        string     Output directory
   "-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 | File containing one or more sequence alignments | Readable sets of sequences | Required | 
| [-intreefile] (Parameter 2) | tree | Phylip tree file (optional) | Phylogenetic tree | |
| [-outfile] (Parameter 3) | outfile | Phylip dnapars program output file | Output file | <*>.fdnapars | 
| Additional (Optional) qualifiers | ||||
| -weights | properties | Weights file | Property value(s) | |
| -maxtrees | integer | Number of trees to save | Integer from 1 to 1000000 | 10000 | 
| -[no]thorough | toggle | More thorough search | Toggle value Yes/No | Yes | 
| -[no]rearrange | boolean | Rearrange on just one best tree | Boolean value Yes/No | Yes | 
| -transversion | boolean | Use transversion parsimony | Boolean value Yes/No | No | 
| -njumble | integer | Number of times to randomise | Integer 0 or more | 0 | 
| -seed | integer | Random number seed between 1 and 32767 (must be odd) | Integer from 1 to 32767 | 1 | 
| -outgrno | integer | Species number to use as outgroup | Integer 0 or more | 0 | 
| -dothreshold | toggle | Use threshold parsimony | Toggle value Yes/No | No | 
| -threshold | float | Threshold value | Number 1.000 or more | 1.0 | 
| -[no]trout | toggle | Write out trees to tree file | Toggle value Yes/No | Yes | 
| -outtreefile | outfile | Phylip tree output file (optional) | Output file | <*>.fdnapars | 
| -printdata | boolean | Print data at start of run | Boolean value Yes/No | No | 
| -[no]progress | boolean | Print indications of progress of run | Boolean value Yes/No | Yes | 
| -stepbox | boolean | Print out steps in each site | Boolean value Yes/No | No | 
| -ancseq | boolean | Print sequences at all nodes of tree | Boolean value Yes/No | No | 
| -[no]treeprint | boolean | Print out tree | Boolean value Yes/No | Yes | 
| -[no]dotdiff | boolean | Use dot differencing to display results | Boolean value Yes/No | Yes | 
| 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 | 
| -scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N | 
| -squick1 -squick_sequence | boolean | Read id and sequence only | Boolean value Yes/No | N | 
| -sformat1 -sformat_sequence | string | Input sequence format | Any string | |
| -iquery1 -iquery_sequence | string | Input query fields or ID list | Any string | |
| -ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0 | 
| -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 | |
| "-outfile" associated outfile qualifiers | ||||
| -odirectory3 -odirectory_outfile | string | Output directory | 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 AACGUGGCCAAAU Beta AAGGUCGCCAAAC Gamma CAUUUCGUCACAA Delta GGUAUUUCGGCCU Epsilon GGGAUCUCGGCCC | 
| 
DNA parsimony algorithm, version 3.69.650
One most parsimonious tree found:
                                            +-----Epsilon   
               +----------------------------3  
  +------------2                            +-------Delta     
  |            |  
  |            +----------------Gamma     
  |  
  1----Beta      
  |  
  +---------Alpha     
requires a total of     19.000
  between      and       length
  -------      ---       ------
     1           2       0.217949
     2           3       0.487179
     3      Epsilon      0.096154
     3      Delta        0.134615
     2      Gamma        0.275641
     1      Beta         0.076923
     1      Alpha        0.173077
 | 
| (((Epsilon:0.09615,Delta:0.13462):0.48718,Gamma:0.27564):0.21795, Beta:0.07692,Alpha:0.17308); | 
| 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 | 
| 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 | Calculate 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.
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