Overview of Broccoli 1.0
Broccoli 1.0
Description
Broccoli version 1.0 with default parameters
Predictions
Upload Date
Tue Nov 26 13:11:02 2019
Coverage
covers all genomes
EggNOG
Description
A database of orthologous groups and functional annotation
Weblink
Predictions
Mapping Log
n/a
Upload Date
Thu Jul 2 16:01:26 2015
Coverage
covers all genomes
EggNOG 5.0 (Fine-grained)
Description
Orthologous pair predictions from OGs refined by phylogentic trees. Three missing species were mapped to closest homolog available.
Weblink
Predictions
Upload Date
Wed Sep 12 16:48:49 2018
Coverage
covers all genomes
EggNOG 5.0 (Groups)
Description
All-vs-all orthologous pair prediction using the smallest compatible OG in the eggNOG level hierarchy for each pair of reference species. Three missing species were mapped using eggNOG 4.5.
Weblink
Predictions
Upload Date
Wed Sep 12 16:29:21 2018
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
Please be aware that the Xenopus tropicalis genes homologies are mostly wrong due to an error in the species tree used in the pipeline
Weblink
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
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
Contact: mateusz.kaduk@scilifelab.se
Predictions
Upload Date
Fri Oct 23 08:28:36 2015
Coverage
covers all genomes
InParanoid
Description
Weblink
Predictions
Mapping Log
n/a
Upload Date
Fri Jun 10 18:50:48 2011
Coverage
covers all genomes
InParanoidCore
Description
Weblink
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.
Consistency score (CS) cut-off of 0.5 was applied.
Weblink
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.
Weblink
Predictions
Mapping Log
n/a
Upload Date
Mon Mar 11 14:17:03 2013
Coverage
covers all genomes
OMA GETHOGs 2.0
Description
Weblink
Predictions
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.
The inference was done on the reference proteomes with the standard parameters.
Weblink
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.
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.
Weblink
Predictions
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.
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.
Weblink
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.
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.
Weblink
Predictions
Upload Date
Wed Jan 25 10:38:19 2017
Coverage
covers all genomes
OrthoFinder 2 (MSA, with DIAMOND)
Description
OrthoFinder 2 using DIAMOND and with MSA tree inference.
Command: "orthofinder -M msa -f 2011_04_reference_proteomes/"
Command: "orthofinder -M msa -f 2011_04_reference_proteomes/"
Predictions
Upload Date
Mon Jul 29 11:08:16 2019
Coverage
covers all genomes
OrthoFinder 2.0 (Defaults, with BLAST)
Description
OrthoFinder 2.0 using BLAST and with default options.
Command: "orthofinder -S blast -f 2011_04_reference_proteomes/"
(defaults: DendroBLAST trees, species tree rooted by STRIDE, new OrthoFinder 2 orthologue inference from gene trees)
Command: "orthofinder -S blast -f 2011_04_reference_proteomes/"
(defaults: DendroBLAST trees, species tree rooted by STRIDE, new OrthoFinder 2 orthologue inference from gene trees)
Predictions
Upload Date
Thu Sep 28 18:43:57 2017
Coverage
covers all genomes
OrthoFinder 2.0 (Defaults, with DIAMOND)
Description
OrthoFinder 2.0 using DIAMOND and with default options.
Command: "orthofinder -S diamond_more_sensitive -f 2011_04_reference_proteomes/"
(defaults: DendroBLAST trees, species tree rooted by STRIDE, new OrthoFinder 2 orthologue inference method from gene trees)
Command: "orthofinder -S diamond_more_sensitive -f 2011_04_reference_proteomes/"
(defaults: DendroBLAST trees, species tree rooted by STRIDE, new OrthoFinder 2 orthologue inference method from gene trees)
Predictions
Upload Date
Thu Sep 28 18:53:03 2017
Coverage
covers all genomes
OrthoFinder 2.0 (MSA, with BLAST)
Description
OrthoFinder 2.0 using BLAST and multiple sequence alignment tree.
Command: "orthofinder -S blast -f -M msa 2011_04_reference_proteomes/"
Command: "orthofinder -S blast -f -M msa 2011_04_reference_proteomes/"
Predictions
Upload Date
Mon Nov 6 15:25:19 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
Weblink
Predictions
Mapping Log
n/a
Upload Date
Sat Feb 16 02:11:22 2013
Coverage
covers all genomes
PANTHER 8.0 (LDO only)
Description
Weblink
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.
Weblink
Predictions
Mapping Log
n/a
Upload Date
Thu Jun 6 11:51:18 2013
Coverage
covers all genomes
Proteinortho 6.0.13
Description
Proteinortho is a tool to detect orthologous genes within different species. For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at one. Details can be found in Lechner et al., BMC Bioinformatics. 2011 Apr 28;12:124.
command used to generate this result:
proteinortho -cpus=32 data/*fasta
(Proteinortho version = 6.0.13)
command used to generate this result:
proteinortho -cpus=32 data/*fasta
(Proteinortho version = 6.0.13)
Predictions
Upload Date
Thu Jan 30 08:24:36 2020
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
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.
This dataset is computed using a divergence parameter of 0.8 and an E-value cutoff of 1e-5.
Weblink
Predictions
Mapping Log
n/a
Upload Date
Wed Feb 8 20:28:20 2012
Coverage
covers all genomes
SonicParanoid (default)
Description
version: 1.0.9
mode: default
Length difference threshold = 0.5
mode: default
Length difference threshold = 0.5
Predictions
Upload Date
Thu May 24 05:23:28 2018
Coverage
covers all genomes
SonicParanoid (fast)
Description
version: 1.0.9
mode: fast
Length difference threshold = 0.5
mode: fast
Length difference threshold = 0.5
Predictions
Upload Date
Wed May 23 16:49:07 2018
Coverage
covers all genomes
SonicParanoid (sensitive)
Description
version: 1.0.9
mode: sensitive
Length difference threshold = 0.5
mode: sensitive
Length difference threshold = 0.5
Predictions
Upload Date
Thu May 24 10:14:56 2018
Coverage
covers all genomes