This repository is an attempt to incorporate the use of BLASTp into BUSCO.

The original modifications made during Fall 2016 are not tracked in this GitHub repo.
Please review the file "pre-GitHub-mods.txt" for a detailed list of modifications prior to tracking.

This process has not been completed as of 4-14-2017.
There are still a few (fixable?) integration issues.
An explanation of the remaining issues is found in "bugs-to-fix.txt".

If you want to run this BUSCO mod on a sample data set, follow the command line instructions in "BUSCO_with_BLASTp.txt".

Author (of modification only): R. Holsapple (raymond.holsapple@gmail.com)
Last update: Spring 2017

Since I am including the original BUSCO (v2.0) code in this repository in addition to my modifications, 
I am including the info from the README file in the BUSCO (v2.0) repo. It is found at the bottom of
this file, below the line.

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NOTE: This public repository is being set up. It provides the **beta version of BUSCO v2.0** that should not be used yet if you intend to use the results in a publication.

* If you want to use the last official release of BUSCO 1.x, please visit http://busco.ezlab.org/

* In the meantime, feel free to test this version that will be officially released soon.

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**BUSCO - Benchmarking sets of Universal Single-Copy Orthologs.**

To get help, ``python BUSCO.py -h`` and ``python BUSCO_plot.py -h``.

See also the user guide: BUSCO_userguide.pdf

You can download BUSCO datasets on http://busco.ezlab.org

*Copyright (C) 2016 E. Zdobnov lab*

BUSCO is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version. See <http://www.gnu.org/licenses/>

BUSCO is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.