README

******************** geneid v.1.0. README File ********************

Summary:
A. What's geneid ?
B. Installing geneid
C. File Listing
D. Compiling geneid
E. To run geneid
F. Authors and help

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A. What's geneid ?
------------------

geneid is a program to predict genic elements as splice sites, exons 
or genes, along eukaryotic DNA sequences. geneid offers also some 
rudimentary support to integrate predictions for multiple sources. 
The program is written in ANSI C, and runs on UNIX operating systems.

Installation, setup and usage of geneid is very easy, and there is a 
range of options to configure output predictions and program behaviour.

geneid source code, compiled binaries and documentation are available 
under the GNU GENERAL PUBLIC LICENSE.

Comments and questions are welcome.      

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B. Installing geneid
--------------------

The geneid distribution contains several directories and files. Source 
code, compiled binaries for a number of architectures and operating 
systems, and documentation files are included in the distribution.

The distribution is archived and compressed in a single file using the
command tar -zcvf. The compressed file name is geneid.tar.gz (or something
similar depending on compiled binaries included). The geneid files can 
be extracted following these instructions:

** UNIX:

Type:
>gzip -d geneid.tar.gz
>tar -xvf geneid.tar

** LINUX:

Type: 
>tar -zxvf geneid.tar.gz

After executing these commands, the directory geneid will be created 
in your working directory. 

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C. File Listing
---------------

The geneid distribution contains the following files and directories:

** bin/
compiled binaries

** docs/
documentation: a short handbook.

** include/
geneid.h: The geneid header file.

** objects/
object files after compiling the source code.

** param/
Parameter files for several species.

** samples/
Test sequences.

** src/
source code of geneid program.

** GNULicense
This software is registered under GNU license.

** Makefile
This file is required to build geneidbinary file.

** README
This file.

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D. Compiling geneid
-------------------

Move into the geneid directory.

Type:
>make 
to compile geneid.

This will generate the geneid executable file within the bin/ subdirectory. 

Type:
>geneid -h 

to test the binary file has been correctly created.

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E. To run geneid
-----------------

To run geneid type:
>geneid -P <parameter_filename> <Sequence_filename>.

Alternatively you can set the parameter file using the environment
variable GENEID.

For example,
>bin/geneid -vP param/human3iso.param samples/example1.fa 

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F. Authors and help
-------------------

geneid has been written by Enrique Blanco and Roderic Guigó (IMIM-UPF).
Parameter files have been generated by Genis Parra and Francisco Camara.

geneid home page is "http://www1.imim.es/software/geneid/index.html" and 
geneid distributions can be obtained through anonymous ftp to 
"ftp.imim.es" in the directory "/pub/software/geneid/".

If you need help, send a message to "geneid@imim.es".