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Hieranoid Hierarchical orthology inference This software is freely available at https://github.com/fabsta/Hieranoid Please read the COPYING file before using this software. If you use Hieranoid please cite: Fabian Schreiber and Erik L.L. Sonnhammer Hieranoid: Hierarchical orthology inference Journal of Molecular Biology (submitted) Installation Checking system requirements - Perl - BioPerl - Usearch or Blastall - HHSearch - Muscle or Kalign Be advised Perl, BioPerl, Blastall, Muscle and Kalign can be installed with 'apt-get install' command HHsearch and Usearch need to be installed manually Perl modules Hieranoid uses Perl modules that are installed in the 'lib' sub-directory of the Hieranoid installation. Please add that directory to your PERL5LIB enviromental variable. In bash you do that the following way: export PERL5LIB=$PERL5LIB:hieranoid_directory/lib Be advised For cluster users, several Perl modules need to be install manually, possibly including: Module::Implementation Module::Runtime Class:Load Class:MOP Sub::Exporter Sub::Install Sub::Name Try::Tiny Package::DeprecationManager Package::Stash Moose Clone Data::OptList Params::Util Configuring Hieranoid Once you have downloaded Hieranoid, you have to tell Hieranoid where to find the required programs. This is done by adapting the settings in the Configuration file (Configurations/Configuration.pm). All options should be explained in greater detail in the Configuration file Starting hieranoid Once, the configuration file has been adapted, the analysis can be started by typing: perl hieranoid.pl Note that depending on the input size, the analysis can take some time Command line arguments Additional options: -c configurationFile -t guide tree file Test dataset: To test the installation, simply type “perl hieranoid.pl”. This will run a quick analysis on the sequences in data/sequences using species tree in data/tree. Program output: All program output is stored in a directory ‘project1’. For each inner node of the provided species tree, a folder will be created in ‘project1/nodes’. Those folders contain several files: The input query files (e.g. Homo_sapiens.fa), Blast results (e.g. Homo_sapiens-Pan_troglodytes), the InParanoid output (sqltable.Homininae) and the orthology predictions (e.g. Homininae.OGTree.txt). Where to put my files: Hieranoid requires a set of sequences as well as a guide tree. By default the Hieranoid searches for the sequences in data/sequences and for the guide tree in data/tree. These options can be changed in the Configuration file. Output: The following is an example of the Hieranoid output format: HieranoidOG-Eukaryota3:((At1g50030.1:1.000,((ENSPTRP00000000280:1.000,ENSP00000354558:1.000)Homininae1:1.000,ENSMUSP00000099510:1.000)Euarchontoglires1:1.000)Eukaryota3:1.000)root; The first is the name of the Hieranoid group followed by a newick string with inparalog scores