Public Projects 2011




Broccoli 1.0



Description
Broccoli, a user-friendly pipeline designed to infer with high precision orthologous groups and pairs of proteins using a phylogeny-based approach. Briefly, Broccoli performs ultra-fast phylogenetic analyses on most proteins and builds a network of orthologous relationships. Orthologous groups are then identified from the network using a parameter-free machine learning algorithm (label propagation). Broccoli is also able to detect chimeric proteins resulting from gene-fusion events and to assign these proteins to the corresponding orthologous groups.
Predictions
Upload Date
2019-11-26T00:00:00Z

EggNOG



Description
A database of orthologous groups and functional annotation
Predictions
Upload Date
2011-07-07T00:00:00Z

EggNOG-5-Fine-grained



Description
Orthologous pair predictions from OGs refined by phylogentic trees. Three missing species were mapped to closest homolog available.
Predictions
Upload Date
2011-07-07T00:00:00Z

EggNOG-5-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.
Predictions
Upload Date
2011-07-07T00:00:00Z

EnsemblCompara (e81)



Description
Ensembl Compara pipeline (version 81) provides cross-species resources and analyses, at both the sequence level and the gene level, with modifications to only use amino-acid models in treebest
Predictions
Upload Date
2011-07-07T00:00:00Z

EnsemblCompara-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
Upload Date
2011-07-07T00:00:00Z

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
Upload Date
2011-07-07T00:00:00Z

Hieranoid 2



Description
Orthology inference method using a hierarchical approach. Hieranoid performs pairwise orthology analysis using InParanoid at each node in a guide tree as it progresses from its leaves to the root. It combines efficient graph-based methodology with aspects of compute-intensive tree-based methods
Predictions
Upload Date
2011-07-07T00:00:00Z

InParanoid



Description
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. Two variants were tested in this study: this one is the regular InParanoid output containing all predicted pairs of orthologs
Predictions
Upload Date
2011-07-07T00:00:00Z

InParanoidCore



Description
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. Two variants were tested in this study: this one is the high-confidence set including only orthologs with InParanoid's maximum confidence score of 1.0
Predictions
Upload Date
2011-07-07T00:00:00Z

MethaPhOrs



Description
MetaPhOrs is a public repository of phylogeny-based orthologs and paralogs that were computed using phylogenetic trees available in twelve public repositories
Predictions
Upload Date
2011-07-07T00:00:00Z

OMA GETHOGs



Description
OMA is a publicly available resource (http://omabrowser.org/) that provides orthology predictions among thousands of proteomes from all domains of life. OMA uses evolutionary distance estimates from Smith���Waterman alignments to infer orthologs. A distinct feature among graph-based methods is the witness of nonorthology step in its pipeline, where cases of differential gene losses get detected. OMA provides three different groupings of orthologs: Pairs, Groups, and HOGs. Here, we constructed hierarchical orthologous groups (OMA HOGs). These are nested groups that contain genes that descend from a single common ancestral gene within a given taxonomic range using the GETHOGs algorithm.
Predictions
Upload Date
2011-07-07T00:00:00Z

OMA Groups



Description
OMA is a publicly available resource (http://omabrowser.org/) that provides orthology predictions among thousands of proteomes from all domains of life. OMA uses evolutionary distance estimates from Smith���Waterman alignments to infer orthologs. A distinct feature among graph-based methods is the witness of nonorthology step in its pipeline, where cases of differential gene losses get detected. OMA provides three different groupings of orthologs: Pairs, Groups, and HOGs. 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.
Predictions
Upload Date
2011-07-07T00:00:00Z

OMA Pairs



Description
OMA is a publicly available resource (http://omabrowser.org/) that provides orthology predictions among thousands of proteomes from all domains of life. OMA uses evolutionary distance estimates from Smith���Waterman alignments to infer orthologs. A distinct feature among graph-based methods is the witness of nonorthology step in its pipeline, where cases of differential gene losses get detected. OMA provides three different groupings of orthologs: Pairs, Groups, and HOGs. The raw pairwise ortholog relationships form the OMA Pairs, a gene-centric view that lists all the orthologs for a given gene. 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
Upload Date
2011-07-07T00:00:00Z

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
Upload Date
2011-07-07T00:00:00Z

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
Upload Date
2011-07-07T00:00:00Z

OrthoFinder-2.0-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)
Predictions
Upload Date
2011-07-07T00:00:00Z

OrthoFinder-2.0-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)
Predictions
Upload Date
2011-07-07T00:00:00Z

OrthoFinder-2.0-MSA



Description
OrthoFinder 2.0 using BLAST and multiple sequence alignment tree.Command: "orthofinder -S blast -f -M msa 2011_04_reference_proteomes/"
Predictions
Upload Date
2011-07-07T00:00:00Z

OrthoInspector 1.30



Description
OrthoInspector30 is a database of precomputed orthology and inparalogy relationships and a stand-alone package allowing large-scale predictions of orthology between thousands of proteomes (http://lbgi.fr/orthoinspector/). The specific version (v1.30) for the Quest for orthologs benchmark used a 1.10-9 blast Evalue threshold. The resource has recently undergone a major new release (2.0), with improved speed and visualisation tools, but the inference algorithm is unchanged from the initial graph-based method.
Predictions
Upload Date
2011-07-07T00:00:00Z

PANTHER 8.0 (all)



Description
The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System was designed to classify proteins (and their genes) in order to facilitate high-throughput analysis. PANTHER ALL will return all orthologs if more than one
Predictions
Upload Date
2011-07-07T00:00:00Z

PANTHER 8.0 (LDO only)



Description
The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System was designed to classify proteins (and their genes) in order to facilitate high-throughput analysis. PANTHER LDO will return only least diverged ortholog for each gene (single best ortholog)
Predictions
Upload Date
2011-07-07T00:00:00Z

PhylomeDB



Description
PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes).
Predictions
Upload Date
2011-07-07T00:00:00Z

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.
Predictions
Upload Date
2020-01-30T00:00:00Z

RBH/BBH



Description
Reciprocal best hits. Classic method consisting of identifying the pairs of genes with mutually highest alignment score between every pair of species. Use reciprocal blastp hits as orthologs, with minimum E-value of 1e���2, keep all hits that are ���99% of the highest score.
Predictions
Upload Date
2011-07-07T00:00:00Z

RSD



Description
Roundup is a large-scale orthology database. The orthologs are computed using the Reciprocal Smallest Distance (RSD) algorithm. Reciprocal Smallest Distance (RSD) is a pairwise orthology algorithm that uses global sequence alignment and maximum likelihood evolutionary distance between sequences to accurately detects orthologs between genomes. This dataset is computed using a divergence parameter of 0.8 and an E-value cutoff of 1e-5.
Predictions
Upload Date
2011-07-07T00:00:00Z

SonicParanoid



Description
version: 1.0.9 mode: sensitive Length difference threshold = 0.5
Predictions
Upload Date
2011-07-07T00:00:00Z

SonicParanoid_fast



Description
version: 1.0.9 mode: sensitive Length difference threshold = 0.5
Predictions
Upload Date
2011-07-07T00:00:00Z

SonicParanoid_sensitive



Description
version: 1.0.9 mode: sensitive Length difference threshold = 0.5
Predictions
Upload Date
2011-07-07T00:00:00Z