Overview of all public projects




EggNOG



Description
A database of orthologous groups and functional annotation
Predictions
Mapping Log
n/a
Upload Date
Thu Jul 2 16:01:26 2015
Coverage
covers all genomes

Ensembl Compara (e56)



Description
Modified version of the vanilla pipeline to build trees with protein sequences only (no nucleotide sequence, no chromosome coordinates).
Please be aware that the Xenopus tropicalis genes homologies are mostly wrong due to an error in the species tree used in the pipeline
Predictions
Mapping Log
n/a
Upload Date
Thu Jun 16 15:26:22 2011
Coverage
covers all genomes

Ensembl Compara (e81)



Description
Ensembl Compara pipeline (version 81) with modifications to only use amino-acid models in treebest
Predictions
Mapping Log
Upload Date
Tue Jan 19 17:53:36 2016
Coverage
covers all genomes

Hieranoid 2



Description
Blast 2.2.18 QfO2011-04 LCA Pairs (SHA d0ffbbe)
Contact: mateusz.kaduk@scilifelab.se
Predictions
Mapping Log
Upload Date
Fri Oct 23 08:28:36 2015
Coverage
covers all genomes

InParanoid



Description
Predictions
Mapping Log
n/a
Upload Date
Fri Jun 10 18:50:48 2011
Coverage
covers all genomes

InParanoidCore



Description
Predictions
Mapping Log
n/a
Upload Date
Tue Jun 14 14:15:46 2011
Coverage
covers all genomes

metaPhOrs



Description
Orthologs were retrieved from trees deposited in: PhylomeDB, Ensembl and EnsemblGenomes, EggNOG, Hogenom and TreeFam.
Consistency score (CS) cut-off of 0.5 was applied.
Predictions
Mapping Log
n/a
Upload Date
Wed Feb 20 09:32:57 2013
Coverage
missing genomes: {PYRKO,STRCO,THEMA}

OMA GETHOGs



Description
Hierarchical Orthologous Groups based on pairwise orthologs infered by OMA. Methodology is described in here, with an alpha parameter set to 0.65.
Predictions
Mapping Log
n/a
Upload Date
Mon Mar 11 14:17:03 2013
Coverage
covers all genomes

OMA GETHOGs 2.0



Description
Hierarchical Orthologous Groups based on pairwise orthologs infered by OMA. The ideas and methodology are described in here, where as this version 2.0 makes use of the new bottom-up algorithm described in here.
Predictions
Mapping Log
Upload Date
Thu Jan 26 00:33:28 2017
Coverage
covers all genomes

OMA Groups (RefSet5)



Description
OMA Groups consists of groups of genes in which all pairs are orthologs. In a graph representation with genes as nodes and orthology relations as edge, OMA groups correspond to fully connected subgraphs. Due to this definition, each OMA group includes at most one sequence per species. The primary intended application of these groups is to provide input data for phylogenetic inference.
The inference was done on the reference proteomes with the standard parameters.
Predictions
Mapping Log
n/a
Upload Date
Mon Jun 6 18:48:45 2011
Coverage
covers all genomes

OMA Groups 2.0



Description
OMA Groups consists of groups of genes in which all pairs are orthologs. In a graph representation with genes as nodes and orthology relations as edge, OMA groups correspond to fully connected subgraphs. Due to this definition, each OMA group includes at most one sequence per species. The primary intended application of these groups is to provide input data for phylogenetic inference.
In this instance of OMA Groups, the pairwise orthologs are based on the relations obtained with the refinements described in OMA 2.0. Additionally, the quasi-cliques that are compatible (no overlapping species) and where at least 50% of the maximal possible edges among the clusters are present, have been merged.
Predictions
Mapping Log
Upload Date
Tue Jul 11 08:41:00 2017
Coverage
covers all genomes

OMA Pairs (Refset5)



Description
The OMA Pairs are the primary product of the OMA pipeline. It is a list of high-confidence pairs of orthologous genes.
OMA is based on an algorithm that compares genes on the basis of evolutionary distances, considers distance inference uncertainty, and accounts for differential gene losses.
Predictions
Mapping Log
n/a
Upload Date
Wed Jun 8 15:18:11 2011
Coverage
covers all genomes

OMA Pairs 2.0



Description
The OMA Pairs are the primary product of the OMA pipeline. It is a list of high-confidence pairs of orthologous genes.
OMA is based on an algorithm that compares genes on the basis of evolutionary distances, considers distance inference uncertainty, and accounts for differential gene losses.
The version 2.0 has better support for fast evolving inparalogs. The changes are described in here.
Predictions
Mapping Log
Upload Date
Wed Jan 25 10:38:19 2017
Coverage
covers all genomes

orthoinspector 1.30 (blast threshold 10-9)



Description
OrthoInspectoris a software system for orthology/paralogy analysis. It uses an original algorithm based on pairwise inparalog group comparison to detect one-to-one, one-to-many and many-to-many orthologous relations. It is made available as an independent software suite facilitating the installation and the maintenance of a database and providing several visualization tools for a comprehensive orthology analysis.
Predictions
Mapping Log
n/a
Upload Date
Fri Jun 10 11:39:26 2011
Coverage
covers all genomes

PANTHER 8.0 (all)



Description
Predictions
Mapping Log
n/a
Upload Date
Sat Feb 16 02:11:22 2013
Coverage
covers all genomes

PANTHER 8.0 (LDO only)



Description
Predictions
Mapping Log
n/a
Upload Date
Fri Feb 15 19:16:56 2013
Coverage
covers all genomes

phylomeDB



Description
PhylomeDB is a public database for complete collections of gene phylogenies (phylomes). Here, we reconstructed 31 phylomes (102-115; 125-133, 205, 206, 210, 219-223) for all 66 species or their subset using various model species as starting point (seed species). In total, 314,086 maximum likelihood trees have been reconstructed, from which 5,567,251 orthologs have been retrieved using Consistency score cut-off of 0.6.
Predictions
Mapping Log
n/a
Upload Date
Thu Jun 6 11:51:18 2013
Coverage
covers all genomes

RBH / BBH



Description
Reciprocal best hits. Use highest scoring reciprocal blastp hits as orthologs. E-value threshold: 1e-2, keep hits >=99% of max_score.
Weblink
Predictions
Mapping Log
Upload Date
Tue Jan 12 16:40:11 2016
Coverage
covers all genomes

RSD 0.8 1e-5 Deluca



Description
Roundup is a large-scale orthology database. The orthologs are computed using the Reciprocal Smallest Distance (RSD) algorithm.
This dataset is computed using a divergence parameter of 0.8 and an E-value cutoff of 1e-5.
Predictions
Mapping Log
n/a
Upload Date
Wed Feb 8 20:28:20 2012
Coverage
covers all genomes

SonicParanoid (default) [50% max-len-diff]



Description
SonicParanoid, default sensitivity, and max allowed length-difference at 50%
Predictions
Mapping Log
Upload Date
Mon Aug 21 17:20:23 2017
Coverage
covers all genomes

SonicParanoid (fast) [50% max-len-diff]



Description
SonicParanoid, fast mode, and max allowed length-difference at 50%
Predictions
Mapping Log
Upload Date
Tue Aug 22 02:40:21 2017
Coverage
covers all genomes

SonicParanoid CORE (default) [50% max-len-diff]



Description
SonicParanoid, CORE set. default sensitivity, and max allowed length-difference at 50%
Predictions
Mapping Log
Upload Date
Mon Aug 21 22:38:45 2017
Coverage
covers all genomes

SonicParanoid CORE (fast) [50% max-len-diff]



Description
SonicParanoid, CORE set, fast mode, and max allowed length-difference at 50%
Predictions
Mapping Log
Upload Date
Tue Aug 22 00:46:32 2017
Coverage
covers all genomes