DarkHorse HGT Candidate Resource
A database of phylogenetically atypical microbial proteins
Program Description: Darkhorse is an experimental program that defines phylogenetic relatedness of BLASTP hits for a set of proteins against the NCBI Genbank nr database, using a lineage probability index (LPI) score. The basic algorithm used to calculate LPI scores and its application in predicting horizontal gene transfer are described in the following publications:
Hardware requirements: Hardware requirements include sufficient disk space to store reference protein sequences, large MySQL relational database tables based on these sequences, and tab-delimited BLASTP sequence comparisons for query sequences. Total disk space required is roughly triple the size of the decompressed protein reference database. Program performance depends primarily on MySQL database access efficiency. A multi-processor CPU with at least 64 GB of RAM is recommended.
Software requirements: DarkHorse is a command-line only program, and requires the Unix OS. It has been installed, tested, and run on multiple versions of Linux and Macintosh OS X platforms. It cannot be run using Microsoft Windows. The following additional third-party software must be pre-installed:
Prior to DarkHorse program installation, a database must be created from within the MySQL program to accept DarkHorse input, e.g.
mysql -u username -p -e "create database db_name;"
The following public database information must be downloaded, de-compressed, and locally available:
The stand-alone software is provided as a unix archive, which must be decompressed and extracted before use:tar -xzvf DarkHorse-2.0_revXX.tar.gz
chmod -R 755 DarkHorse-2.0_revXX
Instructions for installation and use are provided in a README.txt file, which may be downloaded separately below.
Download Current Version
Version 2.0 January 4, 2017
Version 1.5 October 2, 2013
Version 1.4 July 19, 2010
Version 1.3 December 14, 2009
Version 1.2 August 19, 2009
Version 1.1 April 6, 2009
Version 1.0 October 24, 2008
Version 0.9 May 9, 2008
Version 0.8 August 15, 2007