|   | fprotpars | 
Please help by correcting and extending the Wiki pages.
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.
| % 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
| 
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 | 
 | 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 | ||||||||||
| 
     5    10
Alpha     ABCDEFGHIK
Beta      AB--EFGHIK
Gamma     ?BCDSFG*??
Delta     CIKDEFGHIK
Epsilon   DIKDEFGHIK
 | 
| 
    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 
 | 
| 1111100000 0000011111 | 
| 
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
 | 
| ((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.3333]; ((((Epsilon,Delta),Gamma),Beta),Alpha)[0.3333]; (((Epsilon,Delta),(Gamma,Beta)),Alpha)[0.3333]; | 
| 
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........ 
 | 
| (Beta,(Gamma,((Epsilon,Delta),Alpha)))[0.3333]; (Beta,(((Epsilon,Delta),Gamma),Alpha))[0.3333]; (Beta,((Epsilon,Delta),(Gamma,Alpha)))[0.3333]; | 
| 
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
 | 
| ((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]; | 
| 
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
 | 
| ((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]; | 
| 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 | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
Converted (August 2004) to an EMBASSY program by the EMBOSS team.
None