slackbuilds_ponce/academic/ugene

Unipro UGENE is a multiplatform open-source software with the main
goal of assisting molecular biologists without much expertise in
bioinformatics to manage, analyze and visualize their data.

UGENE integrates widely used bioinformatics tools within a common user
interface. The toolkit supports multiple biological data formats and
allows the retrieval of data from remote data sources. It provides
visualization modules for biological objects such as:

- annotated genome sequences;
- Next Generation Sequencing (NGS) assembly data;
- multiple sequence alignments;
- phylogenetic trees;
- 3D structures.

Most of the integrated algorithms are tuned for maximum performance by
the usage of multithreading and special processor instructions. UGENE
includes a visual environment for creating reusable workflows that can
be launched on local resources or in a High Performance Computing
(HPC) environment. UGENE is written in C++ using the Qt framework. The
built-in plugin system and structured UGENE API make it possible to
extend the toolkit with new functionality.

CITING:
If you use UGENE in your work, please quote this publication:
Unipro UGENE: a unified bioinformatics toolkit
Konstantin Okonechnikov, Olga Golosova, Mikhail Fursov, the UGENE team
Bioinformatics 2012 28: 1166-1167 doi: 10.1093/bioinformatics/bts091

NOTE!
While not needed for building of UGENE, the dependencies listed as
"REQUIRED" are highly recommended for the complete functionality of
the program. UGENE will also drive spidey if you have it installed,
but keep in mind that it is available only as a 32-bit binary.

NOTE ABOUT CUDA:
UGENE is built without CUDA support and CUDA-BLAST is not included
among the "REQUIRED", either. Simply, I do not have the hardware. If
someone is interested in such functionality and can offer help with
the script, please contact me.