EMBOSS: efactor

efactor

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Function

Conversion of PHYLIP's factor

Description

EFACTOR - Embossified program to factor multistate characters

Phylip factor documentation.

Usage

Here is a sample session with efactor using the data:-

   4   6   A
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$


% efactor test -options

multistate to binary recoding program
Output file [efactor.outfile]: stdout
put ancestral states in output file [N]: Y
put factors information in output file [N]: 
show progress [Y]: n
    5     8    A
ANCESTOR  ??0?0000
Alpha     11100000
Beta      10001001
Gamma     00011100
Epsilon   11101010

Command line arguments

   Mandatory qualifiers:
  [-datafile]          infile     data file
  [-outfile]           outfile    Output file name

   Optional qualifiers:
   -anc                bool       put ancestral states in output file
   -factors            bool       put factors information in output file
   -[no]progress       bool       show progress

   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default

[-datafile]
(Parameter 1) data file Input file Required

[-outfile]
(Parameter 2) Output file name Output file efactor.outfile

Optional qualifiers Allowed values Default

-anc put ancestral states in output file Yes/No No

-factors put factors information in output file Yes/No No

-[no]progress show progress Yes/No Yes

Advanced qualifiers Allowed values Default

(none)

Mandatory qualifiers	Allowed values	Default
[-datafile] (Parameter 1)	data file	Input file	Required
[-outfile] (Parameter 2)	Output file name	Output file	efactor.outfile
Optional qualifiers	Allowed values	Default
-anc	put ancestral states in output file	Yes/No	No
-factors	put factors information in output file	Yes/No	No
-[no]progress	show progress	Yes/No	Yes
Advanced qualifiers	Allowed values	Default
(none)

Input file format

Output file format

Data files

Notes

References

Warnings

Diagnostics

Exit status

Known bugs

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.