eprotdist

 

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Function

Conversion of PHYLIP's protdist

Description

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

Phylip protdist documentation.

Usage

Here is a sample session with eprotdist using the data:- 
   5   13
Alpha     AACGTGGCCACAT
Beta      AAGGTCGCCACAC
Gamma     CAGTTCGCCACAA
Delta     GAGATTTCCGCCT
Epsilon   GAGATCTCCGCCC


% eprotdist test

Protein distance algorithm
Output file [eprotdist.outfile]: stdout
Method
       Pam : Dayhoff PAM matrix
       Kim : Kimura formula
       Cat : Categories model
Choose the method to use [Pam]: 
    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

Command line arguments 

   Mandatory qualifiers:
  [-msf]               seqset     File containing sequences
  [-outfile]           outfile    Output file name
   -method             list       Choose the method to use

   Optional qualifiers (* if not always prompted):
*  -categ              list       Choose the categorie to use
*  -gencode            list       Which genetic code
*  -prob               float      Prob change category (1.0=easy)
*  -tranrate           float      Transition/transversion ratio
*  -[no]basefrequency  bool       Use empirical base frequencies
*  -freqa              float      Frequency for A
*  -freqc              float      Frequency for C
*  -freqg              float      Frequency for G
*  -freqt              float      Frequency for T/U
   -printdata          bool       Print out the data at start of run
   -progress           bool       Print indications of progress of run

   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default
[-msf]
(Parameter 1)		 File containing sequences Readable sequences Required
[-outfile]
(Parameter 2)		 Output file name Output file eprotdist.outfile
-method Choose the method to use
Pam (Dayhoff PAM matrix)
Kim (Kimura formula)
Cat (Categories model)
 Pam
Optional qualifiers Allowed values Default
-categ Choose the categorie 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 Which genetic code
U (Universal)
M (Mitochondrial)
V (Vertebrate mitochondrial)
F (Fly mitochondrial)
Y (Yeast mitochondrial)
 U
-prob Prob change category (1.0=easy) Number from 0.000 to 1.000 0.457
-tranrate Transition/transversion ratio Number 0.000 or more 2.0
-[no]basefrequency Use empirical base frequencies Yes/No Yes
-freqa Frequency for A Number from 0.000 to 1.000 0.25
-freqc Frequency for C Number from 0.000 to 1.000 0.25
-freqg Frequency for G Number from 0.000 to 1.000 0.25
-freqt Frequency for T/U Number from 0.000 to 1.000 0.25
-printdata Print out the data at start of run Yes/No No
-progress Print indications of progress of run Yes/No No
Advanced qualifiers Allowed values Default
(none)

Data files

Notes

Multiple sequences sets not implemented yet!.

References

Warnings

Diagnostics

Exit status

Known bugs

See also

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.

Priority

Target users

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