INPARANOID: Eukaryotic Ortholog Groups
Release 8.0, December 2013


1. Introduction

InParanoid is a program for automatic identification of orthologs
while differentiating between inparalogs and outparalogs. An
InParanoid cluster is seeded by a reciprocally bestmatching ortholog
pair, around which inparalogs are gathered independently, while
outparalogs are excluded.  The InParanoid database is a collection of
pairwise ortholog groups aiming to include all 'completely sequenced'
eukaryotic genomes. By this we mean above 6X coverage, and less than
1% X letters in the protein sequences.


2. Online access

The InParanoid eukaryotic ortholog database is available both for
direct online access as well as for downloading. Online the user has
the option to view all clusters between two species, search for
clusters based on gene ID or free text search, as well as doing a
blast search based on a sequence. Online access is available at:
http://inparanoid.sbc.su.se.


3. Downloadable content

The current database is available for download at:
http://inparanoid.sbc.su.se/download/current
Previous versions can be found at:
http://inparanoid.sbc.su.se/download/old_versions

Analysed sequences:
Both the original and the processed (i.e. non-redundant, keeping only
the longest transcript) sequences used for analysis can be downloaded 
as fasta files.

Ortholog clusters:
The ortholog clusters for all pairwise species comparisons are
available both as orthoXML (directory orthoXML) as well as tarballs
containing SQL, HTML and raw text files (directory output). For more 
information about orthoXML see: http://www.orthoXML.org. 
Included with the orthoXML files is a schema file called orthoXML.xsd 
that can be used to validate the orthoXML files using xmllint with the 
follwoing command: 

xmllint --noout --schema orthoXML.xsd fileToValidate.orthoXML


4. Database statistics

Version	Date	Species		Species_pairs	Ortholog_groups	Proteins_processed	Orthologous_proteins
2.0	05/03	7		21		57611		165186			86300
3.0	08/04	17		136		559269		303771			236979
4.0	04/05	26		325				463242
5.0	09/06	26		325		1501438		511758			368591
5.1	01/07	26		325		1501438		509483			405433
6.0	09/07	35		595		2642187		610047			501566
6.1	04/08	35		595		2642187		610047			501566
7.0	06/09	100		4950		15240087	1687023			1243926
8.0	12/13	273		37128		79717666	3718323			2999062


5. Algorithmic differences compared to InParanoid 7

For release 8 we have used the program version 4.1. 


6. Stand alone program

InParanoid Version 4.1 is available for download at inparanoid.sbc.su.se.