eprotdist

 

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Function

Protein distance algorithm

Description

EPROTDIST --Embossified program to compute distance matrix from protein sequences

Phylip protdist documentation.

Usage

Here is a sample session with eprotdist 


% eprotdist 
Protein distance algorithm
Input (aligned) protein sequence set: protdist.dat
Method
       Pam : Dayhoff PAM matrix
       Kim : Kimura formula
       Cat : Categories model
Choose the method to use [Pam]: 
Phylip protdist program output file [eprotdist.outfile]:

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

Command line arguments 

Protein distance algorithm
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     File containing sequences
   -method             menu       [Pam] Choose the method to use (Values: Pam
                                  (Dayhoff PAM matrix); Kim (Kimura formula);
                                  Cat (Categories model))
  [-outfile]           outfile    [eprotdist.outfile] Phylip protdist program
                                  output file

   Additional (Optional) qualifiers (* if not always prompted):
*  -categ              menu       [G] Choose the category to use (Values: G
                                  (George/Hunt/Barker (Cys), (Met Val Leu
                                  Ileu), (Gly Ala Ser Thr Pro)); C (Chemical
                                  (Cys Met), (Val Leu Ileu Gly Ala Ser Thr),
                                  (Pro)); H (Hall (Cys), (Met Val Leu Ileu),
                                  (Gly Ala Ser Thr), (Pro)))
*  -gencode            menu       [U] Which genetic code (Values: U
                                  (Universal); M (Mitochondrial); V
                                  (Vertebrate mitochondrial); F (Fly
                                  mitochondrial); Y (Yeast mitochondrial))
*  -prob               float      [0.457] Prob change category (1.0=easy)
                                  (Number from 0.000 to 1.000)
*  -tranrate           float      [2.0] Transition/transversion ratio (Number
                                  0.000 or more)
*  -[no]basefrequency  toggle     [Y] Use empirical base frequencies
*  -freqa              float      [0.25] Frequency for A (Number from 0.000 to
                                  1.000)
*  -freqc              float      [0.25] Frequency for C (Number from 0.000 to
                                  1.000)
*  -freqg              float      [0.25] Frequency for G (Number from 0.000 to
                                  1.000)
*  -freqt              float      [0.25] Frequency for T/U (Number from 0.000
                                  to 1.000)
   -printdata          boolean    [N] Print out the data at start of run
   -progress           boolean    [N] Print indications of progress of run

   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
   -odirectory2        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 sequences Readable set of sequences Required
-method list Choose the method to use
Pam (Dayhoff PAM matrix)
Kim (Kimura formula)
Cat (Categories model)
 Pam
[-outfile]
(Parameter 2)		 outfile Phylip protdist program output file Output file eprotdist.outfile
Additional (Optional) qualifiers
-categ list Choose the category to use
G (George/Hunt/Barker (Cys), (Met Val Leu Ileu), (Gly Ala Ser Thr Pro))
C (Chemical (Cys Met), (Val Leu Ileu Gly Ala Ser Thr), (Pro))
H (Hall (Cys), (Met Val Leu Ileu), (Gly Ala Ser Thr), (Pro))
 G
-gencode list Which genetic code
U (Universal)
M (Mitochondrial)
V (Vertebrate mitochondrial)
F (Fly mitochondrial)
Y (Yeast mitochondrial)
 U
-prob float Prob change category (1.0=easy) Number from 0.000 to 1.000 0.457
-tranrate float Transition/transversion ratio Number 0.000 or more 2.0
-[no]basefrequency toggle Use empirical base frequencies Toggle value Yes/No Yes
-freqa float Frequency for A Number from 0.000 to 1.000 0.25
-freqc float Frequency for C Number from 0.000 to 1.000 0.25
-freqg float Frequency for G Number from 0.000 to 1.000 0.25
-freqt float Frequency for T/U Number from 0.000 to 1.000 0.25
-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
Advanced (Unprompted) qualifiers
(none)
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  
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: protdist.dat

   5   13
Alpha     AACGTGGCCACAT
Beta      AAGGTCGCCACAC
Gamma     CAGTTCGCCACAA
Delta     GAGATTTCCGCCT
Epsilon   GAGATCTCCGCCC

Output file format

Output files for usage example

File: eprotdist.outfile

    5
Alpha          0.00000  0.47285  0.88304  1.29841  2.12269
Beta           0.47285  0.00000  0.45192  1.34185  0.84009
Gamma          0.88304  0.45192  0.00000  1.30693  1.21582
Delta          1.29841  1.34185  1.30693  0.00000  0.27536
Epsilon        2.12269  0.84009  1.21582  0.27536  0.00000

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
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
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 1993 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