| fprotpars

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## Function

Protein parsimony algorithm

## Description

Estimates phylogenies from protein sequences (input using the standard one-letter code for amino acids) using the parsimony method, in a variant which counts only those nucleotide changes that change the amino acid, on the assumption that silent changes are more easily accomplished.

## Algorithm

This program infers an unrooted phylogeny from protein sequences, using a new method intermediate between the approaches of Eck and Dayhoff (1966) and Fitch (1971). Eck and Dayhoff (1966) allowed any amino acid to change to any other, and counted the number of such changes needed to evolve the protein sequences on each given phylogeny. This has the problem that it allows replacements which are not consistent with the genetic code, counting them equally with replacements that are consistent. Fitch, on the other hand, counted the minimum number of nucleotide substitutions that would be needed to achieve the given protein sequences. This counts silent changes equally with those that change the amino acid.

The present method insists that any changes of amino acid be consistent with the genetic code so that, for example, lysine is allowed to change to methionine but not to proline. However, changes between two amino acids via a third are allowed and counted as two changes if each of the two replacements is individually allowed. This sometimes allows changes that at first sight you would think should be outlawed. Thus we can change from phenylalanine to glutamine via leucine in two steps total. Consulting the genetic code, you will find that there is a leucine codon one step away from a phenylalanine codon, and a leucine codon one step away from glutamine. But they are not the same leucine codon. It actually takes three base substitutions to get from either of the phenylalanine codons TTT and TTC to either of the glutamine codons CAA or CAG. Why then does this program count only two? The answer is that recent DNA sequence comparisons seem to show that synonymous changes are considerably faster and easier than ones that change the amino acid. We are assuming that, in effect, synonymous changes occur so much more readily that they need not be counted. Thus, in the chain of changes TTT (Phe) --> CTT (Leu) --> CTA (Leu) --> CAA (Glu), the middle one is not counted because it does not change the amino acid (leucine).

To maintain consistency with the genetic code, it is necessary for the program internally to treat serine as two separate states (ser1 and ser2) since the two groups of serine codons are not adjacent in the code. Changes to the state "deletion" are counted as three steps to prevent the algorithm from assuming unnecessary deletions. The state "unknown" is simply taken to mean that the amino acid, which has not been determined, will in each part of a tree that is evaluated be assumed be whichever one causes the fewest steps.

The assumptions of this method (which has not been described in the literature), are thus something like this:

Change in different sites is independent. Change in different lineages is independent. The probability of a base substitution that changes the amino acid sequence is small over the lengths of time involved in a branch of the phylogeny. 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. 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. The probability of a base change that is synonymous is much higher than the probability of a change that is not synonymous. 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 works by Farris (1983) and Sober (1983a, 1983b, 1988), but also read the exchange between Felsenstein and Sober (1986).

The input for the program is fairly standard. The first line contains the number of species and the number of amino acid positions (counting any stop codons that you want to include).

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.

The protein sequences are given by the one-letter code used by described in the Molecular Sequence Programs documentation file. Note that if two polypeptide chains are being used that are of different length owing to one terminating before the other, they should be coded as (say)

                 HIINMA*????
                 HIPNMGVWABT

since after the stop codon we do not definitely know that there has been a deletion, and do not know what amino acid would have been there. If DNA studies tell us that there is DNA sequence in that region, then we could use "X" rather than "?". Note that "X" means an unknown amino acid, but definitely an amino acid, while "?" could mean either that or a deletion. The distinction is often significant in regions where there are deletions: one may want to encode a six-base deletion as "-?????" since that way the program will only count one deletion, not six deletion events, when the deletion arises. However, if there are overlapping deletions it may not be so easy to know what coding is correct.

One will usually want to use "?" after a stop codon, if one does not know what amino acid is there. If the DNA sequence has been observed there, one probably ought to resist putting in the amino acids that this DNA would code for, and one should use "X" instead, because under the assumptions implicit in this parsimony method, changes to any noncoding sequence are much easier than changes in a coding region that change the amino acid, so that they shouldn't be counted anyway!

The form of this information is the standard one described in the main documentation file. For the U option the tree provided must be a rooted bifurcating tree, with the root placed anywhere you want, since that root placement does not affect anything.

## Usage

Here is a sample session with fprotpars

    % fprotpars
    Protein parsimony algorithm
    Input (aligned) protein sequence set(s): protpars.dat
    Phylip tree file (optional):
    Phylip protpars program output file [protpars.fprotpars]:

    Adding species:
       1. Alpha
       2. Beta
       3. Gamma
       4. Delta
       5. Epsilon

    Doing global rearrangements
      !---------!
       .........
       .........

    Output written to file "protpars.fprotpars"

    Trees also written onto file "protpars.treefile"

    Done.

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

Example 2

    % fprotpars -njumble 3 -seed 3 -printdata -ancseq -whichcode m -stepbox -outgrno 2  -dothreshold -threshold 3
    Protein parsimony algorithm
    Input (aligned) protein sequence set(s): protpars.dat
    Phylip tree file (optional):
    Phylip protpars program output file [protpars.fprotpars]:

    Adding species:
       1. Delta
       2. Epsilon
       3. Alpha
       4. Beta
       5. Gamma

    Doing global rearrangements
      !---------!
       .........
       .........

    Adding species:
       1. Beta
       2. Epsilon
       3. Delta
       4. Alpha
       5. Gamma

    Doing global rearrangements
      !---------!
       .........

    Adding species:
       1. Epsilon
       2. Alpha
       3. Gamma
       4. Delta
       5. Beta

    Doing global rearrangements
      !---------!
       .........

    Output written to file "protpars.fprotpars"

    Trees also written onto file "protpars.treefile"

    Done.

Go to the output files for this example

Example 3

    % fprotpars -njumble 3 -seed 3
    Protein parsimony algorithm
    Input (aligned) protein sequence set(s): protpars2.dat
    Phylip tree file (optional):
    Phylip protpars program output file [protpars2.fprotpars]:

    Data set # 1:

    Adding species:
       1. Delta
       2. Epsilon
       3. Alpha
       4. Beta
       5. Gamma

    Doing global rearrangements
      !---------!
       .........
       .........

    Adding species:
       1. Beta
       2. Epsilon
       3. Delta
       4. Alpha
       5. Gamma

    Doing global rearrangements
      !---------!
       .........

    Adding species:
       1. Epsilon
       2. Alpha
       3. Gamma
       4. Delta
       5. Beta

    Doing global rearrangements
      !---------!
       .........

    Output written to file "protpars2.fprotpars"

    Trees also written onto file "protpars2.treefile"
    Data set # 2:

    Adding species:
       1. Gamma
       2. Delta
       3. Epsilon
       4. Beta
       5. Alpha

    Doing global rearrangements
      !---------!
       .........
       .........

    Adding species:
       1. Alpha
       2. Delta
       3. Epsilon
       4. Gamma
       5. Beta

    Doing global rearrangements
      !---------!
       .........

    Adding species:
       1. Epsilon
       2. Beta
       3. Gamma
       4. Alpha
       5. Delta

    Doing global rearrangements
      !---------!
       .........

    Output written to file "protpars2.fprotpars"

    Trees also written onto file "protpars2.treefile"
    Data set # 3:

    Adding species:
       1. Delta
       2. Beta
       3. Gamma
       4. Alpha
       5. Epsilon

    Doing global rearrangements
      !---------!
       .........
       .........

    Adding species:
       1. Gamma
       2. Delta
       3. Beta
       4. Epsilon
       5. Alpha

    Doing global rearrangements
      !---------!
       .........

    Adding species:
       1. Epsilon
       2. Alpha
       3. Gamma
       4. Delta
       5. Beta

    Doing global rearrangements
      !---------!
       .........

    Output written to file "protpars2.fprotpars"

    Trees also written onto file "protpars2.treefile"

    Done.

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

Example 4

    % fprotpars -option
    Protein parsimony algorithm
    Input (aligned) protein sequence set(s): protpars.dat
    Phylip tree file (optional):
    Phylip weights file (optional): protparswts.dat
    Number of times to randomise [0]:
    Species number to use as outgroup [0]:
    Use threshold parsimony [N]:
    Genetic codes
             U : Universal
             M : Mitochondrial
             V : Vertebrate mitochondrial
             F : Fly mitochondrial
             Y : Yeast mitochondrial
    Use which genetic code [Universal]:
    Phylip protpars program output file [protpars.fprotpars]:
    Write out trees to tree file [Y]:
    Phylip tree output file (optional) [protpars.treefile]:
    Print data at start of run [N]:
    Print indications of progress of run [Y]:
    Print out tree [Y]:
    Print steps at each site [N]:
    Print sequences at all nodes of tree [N]:

    Weights set # 1:

    Adding species:
       1. Delta
       2. Alpha
       3. Gamma
       4. Epsilon
       5. Beta

    Doing global rearrangements
      !---------!
       .........
       .........

    Output written to file "protpars.fprotpars"

    Trees also written onto file "protpars.treefile"

    Weights set # 2:

    Adding species:
       1. Epsilon
       2. Alpha
       3. Delta
       4. Gamma
       5. Beta

    Doing global rearrangements
      !---------!
       .........
       .........

    Output written to file "protpars.fprotpars"

    Trees also written onto file "protpars.treefile"

    Done.

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

## Command line arguments

    Protein 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    [*.fprotpars] Phylip protpars program output
                                      file

       Additional (Optional) qualifiers (* if not always prompted):
       -weights            properties Phylip weights file (optional)
    *  -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] Threshold value (Number 1.000 or more)
       -whichcode          menu       [Universal] Use which genetic code (Values:
                                      U (Universal); M (Mitochondrial); V
                                      (Vertebrate mitochondrial); F (Fly
                                      mitochondrial); Y (Yeast mitochondrial))
       -[no]trout          toggle     [Y] Write out trees to tree file
    *  -outtreefile        outfile    [*.fprotpars] Phylip tree output file
                                      (optional)
       -printdata          boolean    [N] Print data at start of run
       -[no]progress       boolean    [Y] Print indications of progress of run
       -[no]treeprint      boolean    [Y] Print out tree
       -stepbox            boolean    [N] Print steps at each site
       -ancseq             boolean    [N] Print sequences at all nodes of 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 protpars program output file | Output file | <*>.fprotpars
Additional (Optional) qualifiers
-weights | properties | Phylip weights file (optional) | Property value(s) |
-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
-whichcode | list | Use which genetic code |
U | (Universal)
M | (Mitochondrial)
V | (Vertebrate mitochondrial)
F | (Fly mitochondrial)
Y | (Yeast mitochondrial)
| Universal
-[no]trout | toggle | Write out trees to tree file | Toggle value Yes/No | Yes
-outtreefile | outfile | Phylip tree output file (optional) | Output file | <*>.fprotpars
-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
-[no]treeprint | boolean | Print out tree | Boolean value Yes/No | Yes
-stepbox | boolean | Print steps at each site | Boolean value Yes/No | No
-ancseq | boolean | Print sequences at all nodes of tree | Boolean value Yes/No | No
-[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

## Input file format

fprotpars reads any normal sequence USAs.

### Input files for usage example

### File: protpars.dat

         5    10
    Alpha     ABCDEFGHIK
    Beta      AB--EFGHIK
    Gamma     ?BCDSFG*??
    Delta     CIKDEFGHIK
    Epsilon   DIKDEFGHIK

### Input files for usage example 3

### File: protpars2.dat

        5    10
    Alpha     AABBCCCFHK
    Beta      AABB---FHK
    Gamma     ??BBCCCF*?
    Delta     CCIIKKKFHK
    Epsilon   DDIIKKKFHK
        5    10
    Alpha     AADDEGGIIK
    Beta      AA--EGGIIK
    Gamma     ??DDSGG???
    Delta     CCDDEGGIIK
    Epsilon   DDDDEGGIIK
        5    10
    Alpha     AACDDDEGHI
    Beta      AA----EGHI
    Gamma     ??CDDDSG*?
    Delta     CCKDDDEGHI
    Epsilon   DDKDDDEGHI

### Input files for usage example 4

### File: protparswts.dat

    1111100000
    0000011111

## Output file format

fprotpars 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, and (if option 2 is toggled on) a table of the number of changes of state required in each position. 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 "?" there will be multiple equally-parsimonious assignments of states; the user must work these out for themselves by hand. 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 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. 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 positions. 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 positions, and a conclusion as to whether that tree is or is not significantly worse than the best one.

### Output files for usage example

### File: protpars.fprotpars

    Protein parsimony algorithm, version 3.69.650

         3 trees in all found

         +--------Gamma
         !
      +--2     +--Epsilon
      !  !  +--4
      !  +--3  +--Delta
      1     !
      !     +-----Beta
      !
      +-----------Alpha

      remember: this is an unrooted tree!

    requires a total of     16.000

               +--Epsilon
            +--4
         +--3  +--Delta
         !  !
      +--2  +-----Gamma
      !  !
      1  +--------Beta
      !
      +-----------Alpha

      remember: this is an unrooted tree!

    requires a total of     16.000

               +--Epsilon
         +-----4
         !     +--Delta
      +--3
      !  !     +--Gamma
      1  +-----2
      !        +--Beta
      !
      +-----------Alpha

      remember: this is an unrooted tree!

    requires a total of     16.000

### File: protpars.treefile

    ((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.3333];
    ((((Epsilon,Delta),Gamma),Beta),Alpha)[0.3333];
    (((Epsilon,Delta),(Gamma,Beta)),Alpha)[0.3333];

### Output files for usage example 2

### File: protpars.fprotpars

    Protein parsimony algorithm, version 3.69.650

     5 species,  10  sites

    Name          Sequences
    ----          ---------

    Alpha        ABCDEFGHIK
    Beta         ..--......
    Gamma        ?...S..*??
    Delta        CIK.......
    Epsilon      DIK.......

         3 trees in all found

      +-----------Beta
      !
      1  +--------Gamma
      !  !
      +--2     +--Epsilon
         !  +--4
         +--3  +--Delta
            !
            +-----Alpha

      remember: (although rooted by outgroup) this is an unrooted tree!

    requires a total of     14.000

    steps in each position:
             0   1   2   3   4   5   6   7   8   9
         *-----------------------------------------
        0!       3   1   5   3   2   0   0   2   0
       10!   0

    From    To     Any Steps?    State at upper node
                                 ( . means same as in the node below it on tree)

    root     1                AN??EFGHIK
      1   Beta        maybe   .B--......

      [Part of this file has been deleted for brevity]

    root     1                AN??EFGHIK
      1   Beta        maybe   .B--......
      1      2        maybe   ..CD......
      2      3        maybe   ?.........
      3      4         yes    .IK.......
      4   Epsilon     maybe   D.........
      4   Delta        yes    C.........
      3   Gamma        yes    ?B..S..*??
      2   Alpha       maybe   .B........

      +-----------Beta
      !
      1        +--Epsilon
      !  +-----4
      !  !     +--Delta
      +--3
         !     +--Gamma
         +-----2
               +--Alpha

      remember: (although rooted by outgroup) this is an unrooted tree!

    requires a total of     14.000

    steps in each position:
             0   1   2   3   4   5   6   7   8   9
         *-----------------------------------------
        0!       3   1   5   3   2   0   0   2   0
       10!   0

    From    To     Any Steps?    State at upper node
                                 ( . means same as in the node below it on tree)

    root     1                AN??EFGHIK
      1   Beta        maybe   .B--......
      1      3         yes    ..?D......
      3      4         yes    ?IK.......
      4   Epsilon     maybe   D.........
      4   Delta        yes    C.........
      3      2         yes    ..C.......
      2   Gamma        yes    ?B..S..*??
      2   Alpha       maybe   .B........

### File: protpars.treefile

    (Beta,(Gamma,((Epsilon,Delta),Alpha)))[0.3333];
    (Beta,(((Epsilon,Delta),Gamma),Alpha))[0.3333];
    (Beta,((Epsilon,Delta),(Gamma,Alpha)))[0.3333];

### Output files for usage example 3

### File: protpars2.fprotpars

    Protein parsimony algorithm, version 3.69.650

    Data set # 1:

         3 trees in all found

         +--------Gamma
         !
      +--2     +--Epsilon
      !  !  +--4
      !  +--3  +--Delta
      1     !
      !     +-----Beta
      !
      +-----------Alpha

      remember: this is an unrooted tree!

    requires a total of     25.000

               +--Epsilon
            +--4
         +--3  +--Delta
         !  !
      +--2  +-----Gamma
      !  !
      1  +--------Beta
      !
      +-----------Alpha

      remember: this is an unrooted tree!

    requires a total of     25.000

               +--Epsilon
         +-----4

      [Part of this file has been deleted for brevity]

         +--------Gamma
      +--2
      !  !  +-----Epsilon
      !  +--4
      1     !  +--Delta
      !     +--3
      !        +--Beta
      !
      +-----------Alpha

      remember: this is an unrooted tree!

    requires a total of     24.000

               +--Epsilon
            +--4
         +--3  +--Delta
         !  !
      +--2  +-----Gamma
      !  !
      1  +--------Beta
      !
      +-----------Alpha

      remember: this is an unrooted tree!

    requires a total of     24.000

               +--Epsilon
         +-----4
         !     +--Delta
      +--3
      !  !     +--Gamma
      1  +-----2
      !        +--Beta
      !
      +-----------Alpha

      remember: this is an unrooted tree!

    requires a total of     24.000

### File: protpars2.treefile

    ((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.3333];
    ((((Epsilon,Delta),Gamma),Beta),Alpha)[0.3333];
    (((Epsilon,Delta),(Gamma,Beta)),Alpha)[0.3333];
    ((Gamma,(Delta,(Epsilon,Beta))),Alpha)[0.0667];
    (((Epsilon,Gamma),(Delta,Beta)),Alpha)[0.0667];
    ((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.0667];
    ((Epsilon,(Gamma,(Delta,Beta))),Alpha)[0.0667];
    ((Gamma,(Epsilon,(Delta,Beta))),Alpha)[0.0667];
    (((Delta,Gamma),(Epsilon,Beta)),Alpha)[0.0667];
    (((Delta,(Epsilon,Gamma)),Beta),Alpha)[0.0667];
    ((((Epsilon,Delta),Gamma),Beta),Alpha)[0.0667];
    ((Epsilon,((Delta,Gamma),Beta)),Alpha)[0.0667];
    (((Epsilon,(Delta,Gamma)),Beta),Alpha)[0.0667];
    ((Delta,(Gamma,(Epsilon,Beta))),Alpha)[0.0667];
    ((Delta,((Epsilon,Gamma),Beta)),Alpha)[0.0667];
    (((Epsilon,Delta),(Gamma,Beta)),Alpha)[0.0667];
    ((Delta,(Epsilon,(Gamma,Beta))),Alpha)[0.0667];
    ((Epsilon,(Delta,(Gamma,Beta))),Alpha)[0.0667];
    ((Gamma,(Delta,(Epsilon,Beta))),Alpha)[0.2000];
    ((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.2000];
    ((Gamma,(Epsilon,(Delta,Beta))),Alpha)[0.2000];
    ((((Epsilon,Delta),Gamma),Beta),Alpha)[0.2000];
    (((Epsilon,Delta),(Gamma,Beta)),Alpha)[0.2000];

### Output files for usage example 4

### File: protpars.fprotpars

    Protein parsimony algorithm, version 3.69.650

    Weights set # 1:

         3 trees in all found

         +--------Gamma
         !
      +--2     +--Epsilon
      !  !  +--4
      !  +--3  +--Delta
      1     !
      !     +-----Beta
      !
      +-----------Alpha

      remember: this is an unrooted tree!

    requires a total of     14.000

               +--Epsilon
            +--4
         +--3  +--Delta
         !  !
      +--2  +-----Gamma
      !  !
      1  +--------Beta
      !
      +-----------Alpha

      remember: this is an unrooted tree!

    requires a total of     14.000

      [Part of this file has been deleted for brevity]

               +--Epsilon
         +-----4
         !     +--Delta
      +--3
      !  !     +--Gamma
      1  +-----2
      !        +--Beta
      !
      +-----------Alpha

      remember: this is an unrooted tree!

    requires a total of      2.000

         +--------Delta
      +--3
      !  !  +-----Epsilon
      !  +--4
      1     !  +--Gamma
      !     +--2
      !        +--Beta
      !
      +-----------Alpha

      remember: this is an unrooted tree!

    requires a total of      2.000

         +--------Epsilon
      +--4
      !  !  +-----Delta
      !  +--3
      1     !  +--Gamma
      !     +--2
      !        +--Beta
      !
      +-----------Alpha

      remember: this is an unrooted tree!

    requires a total of      2.000

### File: protpars.treefile

    ((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.3333];
    ((((Epsilon,Delta),Gamma),Beta),Alpha)[0.3333];
    (((Epsilon,Delta),(Gamma,Beta)),Alpha)[0.3333];
    ((Gamma,(Delta,(Epsilon,Beta))),Alpha)[0.0667];
    (((Epsilon,Gamma),(Delta,Beta)),Alpha)[0.0667];
    ((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.0667];
    ((Epsilon,(Gamma,(Delta,Beta))),Alpha)[0.0667];
    ((Gamma,(Epsilon,(Delta,Beta))),Alpha)[0.0667];
    (((Delta,Gamma),(Epsilon,Beta)),Alpha)[0.0667];
    (((Delta,(Epsilon,Gamma)),Beta),Alpha)[0.0667];
    ((((Epsilon,Delta),Gamma),Beta),Alpha)[0.0667];
    ((Epsilon,((Delta,Gamma),Beta)),Alpha)[0.0667];
    (((Epsilon,(Delta,Gamma)),Beta),Alpha)[0.0667];
    ((Delta,(Gamma,(Epsilon,Beta))),Alpha)[0.0667];
    ((Delta,((Epsilon,Gamma),Beta)),Alpha)[0.0667];
    (((Epsilon,Delta),(Gamma,Beta)),Alpha)[0.0667];
    ((Delta,(Epsilon,(Gamma,Beta))),Alpha)[0.0667];
    ((Epsilon,(Delta,(Gamma,Beta))),Alpha)[0.0667];

## 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 | Estimate nucleotide phylogeny by maximum likelihood
fdnamlk | Estimates nucleotide phylogeny by maximum likelihood
fdnamove | Interactive DNA parsimony
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
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

## 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.

## Comments

    None