                                  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


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 (c) 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
