Hieranoid 2 - Hierarchical orthology inference algorithm

About

• 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).

Installation

1. 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).

2. Clone the source code from the repository

   git clone https://bitbucket.org/mkaduk/hieranoid-2
   

3. 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
   

Configuration

Minimal configuration to get started

1. 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.

2. 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";
   

3. 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