Hieranoid 2 - Hierarchical orthology inference algorithm
- Hieranoid 2 is a continuation of Fabian Schreiber work and the fork of original repository.
- Hieranoid 1 was published in Journal of Molecular Biology (DOI: 10.1016/j.jmb.2013.02.018).
On GNU/Linux distribution such as Debian or Ubuntu, external programs can be installed by
sudo apt-get install blast2 muscle hhsuite kalign git
Hieranoid 2 was tested with blast2 (2.2.18), muscle (3.8.31).
Clone the source code from the repository
git clone https://bitbucket.org/mkaduk/hieranoid-2
Prepare perl enviroment where you intend to run Hieranoid 2.
Note: Perl allow for compiled libraries which are specific for hardware architecture where they were installed.
Basic setup of perl enviroment
# Bootstrap locally perl 5.20.1 wget -O - http://install.perlbrew.pl --no-check-certificate | bash source ~/perl5/perlbrew/etc/bashrc perlbrew --notest install perl-5.20.1 perlbrew switch perl-5.20.1 perlbrew install-cpanm # Use cpanm from perlbrew to install required modules perlbrew exec cpanm BioPerl perlbrew exec cpanm Bio::Phylo perlbrew exec cpanm Moose perlbrew exec cpanm Log::Log4perl perlbrew exec cpanm Net::OpenSSH::Parallel perlbrew exec cpanm XML::LibXML perlbrew exec cpanm XML::Parser
Minimal configuration to get started
Create project subdirectories
mkdir mkad # Create project directory mkdir mkad/log mkdir mkad/sequences mkdir mkad/tree
Copy your proteomes in fasta format, guide tree to corresponding directories.
Note: Names of branches in guidetree in Newick format, must be the same as proteoms file names without an extension.
Set project details in configuration file
nano lib/Configurations/Configuration.pm $rootDirectory = "/scratch/Hieranoid2/"; $projectName = "mkad"; $tempDir = "/scratch/temp/; $speciesFilesDirectory = "$rootDirectory/mkad/sequences-short/"; $treeFile = "$rootDirectory/mkad/tree/fungi5-short.tre";
Set up external programs
External programs are usually placed in extern directory and depend on configuration. Hieranoid 2.0 was tested with usearch5.1 in combination with segmasker (from blast 2.2.28), blastall (from blast 2.2.18) and muscle 3.8.31.
Listing of extern directory
muscle muscle3.8.31_i86linux64 blast-2.2.18/ usearch5.1 usearch5.1.221_i86linux32
After populating extern directory, correct paths must be set in aforementioned Configuration.pm file.
Running Hieranoid 2
To run Hieranoid perlbrew enviroment was used, but any other perl installation is acceptable. Example run would look like
source ~/perl5/perlbrew/etc/bashrc # Load perlbrew enviroment perlbrew exec perl -I ./lib ./hieranoid.pl