## EMBOSS: efactor

# Program efactor

## 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)

## Input file format

## Output file format

## Data files

## Notes

## References

## Warnings

## Diagnostics

## Exit status

## Known bugs

## See also

## 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.

## Priority

## Target users

## Comments