CSC

fdnapars

 

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Function

DNA parsimony algorithm

Description

Estimates phylogenies by the parsimony method using nucleic acid sequences. Allows use the full IUB ambiguity codes, and estimates ancestral nucleotide states. Gaps treated as a fifth nucleotide state. It can also fo transversion parsimony. Can cope with multifurcations, reconstruct ancestral states, use 0/1 character weights, and infer branch lengths

Algorithm

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 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, 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.

Usage

Here is a sample session with fdnapars

% 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

Command line arguments

DNA parsimony algorithm Version: EMBOSS:6.3.0 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

Input file format

fdnapars reads any normal sequence USAs.

Input files for usage example

File: dnapars.dat

5 13 Alpha AACGUGGCCAAAU Beta AAGGUCGCCAAAC Gamma CAUUUCGUCACAA Delta GGUAUUUCGGCCU Epsilon GGGAUCUCGGCCC

Output file format

fdnapars output is standard: if option 1 is toggled on, the data is printed out, with the convention that "." means "the same as in the first species". Then comes a list of equally parsimonious trees. Each tree has branch lengths. These are computed using an algorithm published by Hochbaum and Pathria (1997) which I first heard of from Wayne Maddison who invented it independently of them. This algorithm averages the number of reconstructed changes of state over all sites a over all possible most parsimonious placements of the changes of state among branches. Note that it does not correct in any way for multiple changes that overlay each other. If option 2 is toggled on a table of the number of changes of state required in each character is also printed. If option 5 is toggled on, a table is printed out after each tree, showing for each branch whether there are known to be changes in the branch, and what the states are inferred to have been at the top end of the branch. This is a reconstruction of the ancestral sequences in the tree. If you choose option 5, a menu item "." appears which gives you the opportunity to turn off dot-differencing so that complete ancestral sequences are shown. If the inferred state is a "?" or one of the IUB ambiguity symbols, there will be multiple equally-parsimonious assignments of states; the user must work these out for themselves by hand. A "?" in the reconstructed states means that in addition to one or more bases, a deletion may or may not be present. If option 6 is left in its default state the trees found will be written to a tree file, so that they are available to be used in other programs. If the U (User Tree) option is used and more than one tree is supplied, the program also performs a statistical test of each of these trees against the best tree. This test, which is a version of the test proposed by Alan Templeton (1983) and evaluated in a test case by me (1985a). It is closely parallel to a test using log likelihood differences due to Kishino and Hasegawa (1989), and uses the mean and variance of step differences between trees, taken across sites. If the mean is more than 1.96 standard deviations different then the trees are declared significantly different. The program prints out a table of the steps for each tree, the differences of each from the best one, the variance of that quantity as determined by the step differences at individual sites, and a conclusion as to whether that tree is or is not significantly worse than the best one. If the U (User Tree) option is used and more than one tree is supplied, and the program is not told to assume autocorrelation between the rates at different sites, the program also performs a statistical test of each of these trees against the one with highest likelihood. If there are two user trees, this is a version of the test proposed by Alan Templeton (1983) and evaluated in a test case by me (1985a). It is closely parallel to a test using log likelihood differences due to Kishino and Hasegawa (1989) It uses the mean and variance of the differences in the number of steps between trees, taken across sites. If the two trees' means are more than 1.96 standard deviations different, then the trees are declared significantly different. If there are more than two trees, the test done is an extension of the KHT test, due to Shimodaira and Hasegawa (1999). They pointed out that a correction for the number of trees was necessary, and they introduced a resampling method to make this correction. In the version used here the variances and covariances of the sums of steps across sites are computed for all pairs of trees. To test whether the difference between each tree and the best one is larger than could have been expected if they all had the same expected number of steps, numbers of steps for all trees are sampled with these covariances and equal means (Shimodaira and Hasegawa's "least favorable hypothesis"), and a P value is computed from the fraction of times the difference between the tree's value and the lowest number of steps exceeds that actually observed. Note that this sampling needs random numbers, and so the program will prompt the user for a random number seed if one has not already been supplied. With the two-tree KHT test no random numbers are used. In either the KHT or the SH test the program prints out a table of the number of steps for each tree, the differences of each from the lowest one, the variance of that quantity as determined by the differences of the numbers of steps at individual sites, and a conclusion as to whether that tree is or is not significantly worse than the best one. Option 6 in the menu controls whether the tree estimated by the program is written onto a tree file. The default name of this output tree file is "outtree". If the U option is in effect, all the user-defined trees are written to the output tree file. If the program finds multiple trees tied for best, all of these are written out onto the output tree file. Each is followed by a numerical weight in square brackets (such as [0.25000]). This is needed when we use the trees to make a consensus tree of the results of bootstrapping or jackknifing, to avoid overrepresenting replicates that find many tied trees.

Output files for usage example

File: dnapars.fdnapars

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

File: dnapars.treefile

(((Epsilon:0.09615,Delta:0.13462):0.48718,Gamma:0.27564):0.21795, Beta:0.07692,Alpha:0.17308);

Data files

None

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

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

Author(s)

This program is an EMBOSS conversion of a program written by Joe Felsenstein as part of his PHYLIP package.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Written (2004) - Joe Felsenstein, University of Washington.

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

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.