
                                 fprotpars 



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"


   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 -outgrn
o 2  -thresh -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"


   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"


   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"


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

Command line arguments

   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)
   -thresh             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
   -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 standard output
   -filter             boolean    Read standard input, write 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. 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

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 3.6b



     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 3.6b

 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 3.6b


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 3.6b




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)[0.0714];
(((Epsilon,Gamma),(Delta,Beta)),Alpha)[0.0714];
((Epsilon,(Gamma,(Delta,Beta))),Alpha)[0.0714];
((Gamma,(Epsilon,(Delta,Beta))),Alpha)[0.0714];
(((Delta,Gamma),(Epsilon,Beta)),Alpha)[0.0714];
(((Delta,(Epsilon,Gamma)),Beta),Alpha)[0.0714];
((((Epsilon,Delta),Gamma),Beta),Alpha)[0.0714];
((Epsilon,((Delta,Gamma),Beta)),Alpha)[0.0714];
(((Epsilon,(Delta,Gamma)),Beta),Alpha)[0.0714];
((Delta,(Gamma,(Epsilon,Beta))),Alpha)[0.0714];
((Delta,((Epsilon,Gamma),Beta)),Alpha)[0.0714];
(((Epsilon,Delta),(Gamma,Beta)),Alpha)[0.0714];
((Delta,(Epsilon,(Gamma,Beta))),Alpha)[0.0714];
((Epsilon,(Delta,(Gamma,Beta))),Alpha)[0.0714];

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      Creates a distance matrix from multiple alignments
   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
   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    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.

   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.

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.
