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. |
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DNA parsimony algorithm Version: EMBOSS:6.2.0 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) -thresh 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 -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 "-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 |
-thresh | 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 |
-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 | |
"-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 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 | Estimates 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 | Distance matrix from restriction sites or fragments |
frestml | Restriction site maximum Likelihood method |
fseqboot | Bootstrapped sequences algorithm |
fseqbootall | Bootstrapped sequences algorithm |
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.
Converted (August 2004) to an EMBASSY program by the EMBOSS team.