Public Projects 2020

Description

Domainoid is a program for automatic identification of domain-based orthologs. Domainoid builds on top of the InParanoid algorithm, and uses domains from Pfam to infer orthologs on a domain level. The domain-level-orhtologs have been reconstructed on the full protein level in order to be compatible with the benchmark, using an alpha threshold of 0.4. The Domainoid orthologs are used to enrich orthologs from InParanoid.

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2022-02-05T14:50:26+00:00

Description

Ensembl Compara pipeline (version 103) provides cross-species resources and analyses, at both the sequence level and the gene level. Gene families are inferred using a hybrid approach combining TreeFam and PANTHER HMM classification, and all-against-all BLAST search for the sequences without HMM matches.

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2022-02-05T16:44:39+00:00

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

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2022-12-16T09:16:52+00:00

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

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2022-12-16T09:20:13+00:00

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

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2022-12-16T09:00:24+00:00

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

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2022-12-16T09:06:03+00:00

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

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2022-12-16T09:12:11+00:00

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

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2022-12-16T09:26:45+00:00

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

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2022-02-05T14:58:38+00:00

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

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2022-02-05T14:54:12+00:00

Description

MetaPhOrs is a public repository of phylogeny-based orthologs and paralogs that were computed using phylogenetic trees available in twelve public repositories

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2022-02-05T16:29:27+00:00

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.

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2022-02-05T13:37:30+00:00

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.

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2022-02-05T13:40:54+00:00

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.

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2022-02-05T13:44:37+00:00

Description

OrthoFinder 2.5.2 using BLAST and multiple sequence alignment tree.Command: "orthofinder -S blast -f -M msa 2011_04_reference_proteomes/"

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2022-02-05T16:26:29+00:00

Description

OrthoInspector 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.

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2022-02-05T16:48:50+00:00

Description

OrthoMCL provides a scalable method for constructing orthologous groups across a wide range of species in Eukaryota, Bacteria, and Archaea. The algorithm calculates Blast scores between every pair of proteins in order to identify putative orthologs and paralogs. The Blast scores are normalized to account for betwen-species sequence divergence. Then, OrthoMCL employs a Markov Cluster algorithm to appropriately group closely-related orthologs and paralogs. We find that groups containing proteins with previously assigned EC annotations exhibit a high degree of EC consistency, showing OrthoMCL's utility for automated eukaryotic genome annotation.

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2022-02-05T16:37:37+00:00

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)

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2022-02-05T13:55:11+00:00

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)

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2022-02-05T13:49:30+00:00

Description

PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes).

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2022-02-05T16:32:06+00:00

Description

Proteinortho v5.16b with BLAST in the default configuration. The input was the QfO2020.2 dataset subsetted to the proteomes (without additional files). The upload type is a list of pairwise orthologs. Details can be found in Lechner et al., BMC Bioinformatics. 2011 Apr 28;12:124 doi=10.1186/1471-2105-12-124

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2023-08-09T09:19:10+00:00

Description

Proteinortho v6.3.0 in pseudo modus using diamond v2.0.15 with sensitivity option (this configuration represents the default settings for Proteinortho6). The input was the QfO2020.2 dataset subsetted to the proteomes (without additional files). The upload type is a list of pairwise orthologs.

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2023-08-09T09:23:43+00:00

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.

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2022-02-05T13:09:50+00:00

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.

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2022-02-05T12:57:13+00:00

Description

version: 1.0.9 mode: sensitive Length difference threshold = 0.5

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2022-02-05T13:57:48+00:00

Description

version: 1.0.9 mode: sensitive Length difference threshold = 0.5

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2022-02-05T14:00:09+00:00

Description

version 1.2.6

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2022-02-05T14:02:54+00:00

Description

version: 1.0.9 mode: sensitive Length difference threshold = 0.5

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2022-02-05T14:05:14+00:00