eprotpars

 

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Function

Protein parsimony algorithm

Description

EPROTPARS -- Embossified Protein Sequence Parsimony Method

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 UUU and UUC 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 UUU (Phe) --> CUU (Leu) --> CUA (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 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:

       1.  Change in different sites is independent.

       2.  Change in different lineages is independent.

       3.  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.

       4.  The  expected  amounts  of  change  in  different  branches  of  the
          phylogeny  do  not  vary  by  so much that two changes in a high-rate
          branch are more probable than one change in a low-rate branch.

       5.  The expected amounts of change do not vary enough among  sites  that
          two changes in one site are more probable than one change in another.

       6.  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 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!

Usage

Here is a sample session with eprotpars


% eprotpars 
Protein parsimony algorithm
Input (aligned) protein sequence set: protpars.dat
Randomize input order of species [N]: 
Phylip protpars program output file [eprotpars.outfile]: 
Create a tree file [Y]: 
Phylip tree output file [eprotpars.treefile]: 

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 (* if not always prompted):
  [-sequence]          seqset     File containing a sequence alignment
*  -random             toggle     [N] Randomize input order of species
*  -randseed           integer    [3] Random number seed (must be odd) (Any
                                  integer value)
*  -randtimes          integer    [3] How many times to randomise (Any integer
                                  value)
*  -outgnum            integer    [1] Number of the outgroup (Integer 1 or
                                  more)
*  -valthresh          float      [1.0] Threshold value (Number 1.000 or more)
  [-outfile]           outfile    [eprotpars.outfile] Phylip protpars program
                                  output file
  [-[no]trout]         toggle     [Y] Create a tree file
*  -treefile           outfile    [eprotpars.treefile] Phylip tree output file

   Additional (Optional) qualifiers:
   -[no]besttree       toggle     [Y] Search for best tree
   -og                 toggle     [N] Outgroup root
   -printdata          boolean    [N] Print out the data at start of run
   -progress           boolean    [N] Print indications of progress of run
   -steps              boolean    [N] Print out steps in each site
   -seqatnodes         boolean    [N] Print sequences at all nodes of tree
   -[no]drawtree       boolean    [Y] Draw tree

   Advanced (Unprompted) qualifiers:
   -thresh             toggle     [N] Use Threshold parsimony

   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
   -odirectory2        string     Output directory

   "-treefile" 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)
seqset File containing a sequence alignment Readable set of sequences Required
-random toggle Randomize input order of species Toggle value Yes/No No
-randseed integer Random number seed (must be odd) Any integer value 3
-randtimes integer How many times to randomise Any integer value 3
-outgnum integer Number of the outgroup Integer 1 or more 1
-valthresh float Threshold value Number 1.000 or more 1.0
[-outfile]
(Parameter 2)
outfile Phylip protpars program output file Output file eprotpars.outfile
[-[no]trout]
(Parameter 3)
toggle Create a tree file Toggle value Yes/No Yes
-treefile outfile Phylip tree output file Output file eprotpars.treefile
Additional (Optional) qualifiers
-[no]besttree toggle Search for best tree Toggle value Yes/No Yes
-og toggle Outgroup root Toggle value Yes/No No
-printdata boolean Print out the data at start of run Boolean value Yes/No No
-progress boolean Print indications of progress of run Boolean value Yes/No No
-steps boolean Print out steps in each site Boolean value Yes/No No
-seqatnodes boolean Print sequences at all nodes of tree Boolean value Yes/No No
-[no]drawtree boolean Draw tree Boolean value Yes/No Yes
Advanced (Unprompted) qualifiers
-thresh toggle Use Threshold parsimony Toggle value Yes/No No
Associated qualifiers
"-sequence" associated seqset 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
-odirectory2
-odirectory_outfile
string Output directory Any string  
"-treefile" 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

Input files for usage example

File: protpars.dat

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

Output file format

Output files for usage example

File: eprotpars.outfile



     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: eprotpars.treefile

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

Data files

None.

Notes

Multiple sequences sets not implemented yet!.

References

None.

Warnings

None.

Diagnostics

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
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
fprotpars Protein parsimony 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)

(c) Copyright 1986-1993 by Joseph Felsenstein and by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.

This application was modified for inclusion in EMBOSS by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

History

Target users

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

Comments

None