eprotpars

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Function

Description

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.

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

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

% 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

Notes

References

Warnings

Diagnostics

Exit status

Known bugs

See also

Author(s)

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

Comments

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