efactor

 

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Function

Multistate to binary recoding program

Description

EFACTOR - Embossified program to factor multistate characters

Phylip factor documentation.

Usage

Here is a sample session with efactor 


% efactor 
Multistate to binary recoding program
Phylip factor program input file: factor.dat
Phylip factor program output file [efactor.outfile]: 


Data matrix written on output file

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

Command line arguments 

Multistate to binary recoding program
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers:
  [-datafile]          infile     Phylip factor program input file
  [-outfile]           outfile    [efactor.outfile] Phylip factor program
                                  output file

   Additional (Optional) qualifiers:
   -anc                boolean    [N] Put ancestral states in output file
   -factors            boolean    [N] Put factors information in output file
   -[no]progress       boolean    [Y] Show progress

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-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
[-datafile]
(Parameter 1)		 infile Phylip factor program input file Input file Required
[-outfile]
(Parameter 2)		 outfile Phylip factor program output file Output file efactor.outfile
Additional (Optional) qualifiers
-anc boolean Put ancestral states in output file Boolean value Yes/No No
-factors boolean Put factors information in output file Boolean value Yes/No No
-[no]progress boolean Show progress Boolean value Yes/No Yes
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-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: factor.dat

   4   6
1 A:B B:C
2 A:B B:.
4
5 0:1 1:2 .:0
6 .:# #:$ #:%
999
Alpha     CAW00#
Beta      BBX01%
Gamma     ABY12#
Epsilon   CAZ01$

Output file format

Output files for usage example

File: efactor.outfile

    4     8
Alpha     11100000
Beta      10001001
Gamma     00011100
Epsilon   11101010

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostics

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description
eclique Largest clique program
edollop Dollo and polymorphism parsimony algorithm
edolpenny Penny algorithm Dollo or polymorphism
emix Mixed parsimony algorithm
epenny Penny algorithm, branch-and-bound
fclique Largest clique program
fdollop Dollo and polymorphism parsimony algorithm
fdolpenny Penny algorithm Dollo or polymorphism
ffactor Multistate to binary recoding program
fmix Mixed parsimony algorithm
fmove Interactive mixed method parsimony
fpars Discrete character parsimony
fpenny Penny algorithm, branch-and-bound

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