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For more information on how to install, train and run geneid check the Wiki

******************** geneid v.1.4.5 README File ********************

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

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.

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.

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 geneid binary file.

** README This file.

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.

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

F. Authors and help

geneid has been written by Enrique Blanco, Tyler Alioto and Roderic Guigó (CRG). Parameter files have been generated by Genis Parra, Francisco Camara and Tyler Alioto.

geneid home page is "http://genome.crg.es/software/geneid" and geneid distributions can be obtained via github at "https://github.com/guigolab/geneid".

If you need help, send a message to "[email protected]".