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Welcome to the deltaBS wiki!

Getting started

Download the source code, then follow the instructions below to get started:

To run, you need to have HMMER3 installed (http://hmmer.janelia.org/), and you need BioPerl (http://bioperl.org/INSTALL.html). DeltaBS also requires the follow modules: Statistics::Distributions, Data::Dumper, and Getopt::Long. These can be installed via CPAN.

You also need to download an HMM collection. You can download the Pfam collection from ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release (we use Pfam-A.hmm). This will produce conservative results, in which only very likely loss of function mutations will be flagged. Alternatively, you can download a set of taxon-specific HMMs from eggNOG: http://eggnog5.embl.de/#/app/downloads. Note you may also use your own HMM library, if you so choose.

Once you have downloaded the HMMs, store them all in a single concatenated file. hmmpress must be used once to prepare the HMM database for use:

`hmmpress <hmm_file.hmm>`

Next, proceed to the instructions for either running the analysis on a population or for pairwise comparisons.