Public Projects 2022

Description

Reciprocal best hits. Classic method consisting of identifying the pairs of genes with mutually highest alignment score between every pair of species. Uses Smith-Waterman optimal pairwise alignments, with a minimum E-value of 1e-2. All hits that reach >= 99% of the highest score are kept as inparalogs.

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2023-07-10T15:02:52Z

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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2023-07-04T15:59:57Z

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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2023-10-11T13:43:48Z

Description

FastOMA is a scalable software package to infer orthology relationship

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2023-12-05T13:02:47Z

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 and computed with OmaStandalone v2.5.

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2023-07-10T15:10:40Z

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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2023-07-10T15:15:39Z

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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2023-11-01T11:38:26Z

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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2023-11-06T14:31:17Z

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 and computed with OmaStandalone v2.5. 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.

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2023-07-10T15:45:45Z

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, and it is computed with OmaStandalone v2.5. The changes are described in here.

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2023-07-10T15:41:25Z

Description

Family Free Genome Comparison (FFGC) is a self-contained workflow system that provides functionality for all steps of a family-free gene order analysis starting from annotated genome sequences. Family-free methods for gene order analyses do not require prior knowledge of evolutionary relationships between the genes across the studied genomes. This tool features a complete workflow for genome comparison, requiring nothing but annotated genome sequences as input. Surprisingly, the continuous development of family-free methods recently lead to an integrated method for inferring gene families across several species. FFGC now includes a subworkflow for inferring gene families simultaneously based on gene similarities and family-free genome rearrangements (OrthoFFGCʜ and OrthoFFGCʜ≈ extensions).

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2023-11-01T16:15:13Z

Description

OrthoFinder 2.5.5 using BLAST and multiple sequence alignment tree.Command: "orthofinder -S blast -f -M msa reference_proteomes/"

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2023-12-05T13:08:32Z

Description

OrthoInspector is one of the leading software suites for orthology relations inference. Distributions of protein orthologs are represented by heatmaps summarizing their evolutionary histories, and proteins with similar profiles can be directly accessed. Two novel tools have been implemented for comparative genomics: a phylogenetic profile search that can be used to find proteins with a specific presence-absence profile and investigate their functions and, inversely, a GO profiling tool aimed at deciphering evolutionary histories of molecular functions, processes or cell components. In addition to the re-designed website, the OrthoInspector resource now provides a REST interface for programmatic access. OrthoInspector 3.0 is available at http://lbgi.fr/orthoinspectorv3.

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2023-10-04T14:38:08Z

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

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2023-10-31T11:11:44Z

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

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2023-10-31T11:06:46Z

Description

A database of orthologous groups and functional annotation. The pipeline starts with mapping all target sequences in the database against the Pfam database, creating groups of protein sequences that consistently align with at least one known domain. These groups of sequences that share a Pfam domain are referred to as 'protein families' from this point onwards. Multidomain proteins will therefore appear in as many families as the number of Pfam domains they contain, and all sequences within a protein family will contain at least one shared domain. This strategy prevents non-alignable proteins from being grouped together in the same cluster, as we previously observed occurring with protein families containing promiscuous domains. Furthermore, it provides a domain-centric view of the orthology relationships within each set, enabling multidomain proteins to be recruited into different families. All protein sequences without a detectable Pfam domain are clustered de novo based on MMseqs, producing a large pool of putative protein families. Next, to identify OGs within each protein family cluster, a multiple sequence alignment and a phylogenetic tree are inferred for each cluster. We aligned sequences using MAFFT (<1000 sequences) or FAMSA (larger protein sets), removed uninformative alignment columns using an ad hoc script, inferred phylogenetic trees using FastTree2, and rooted using the Minimum variance method from the FastRoot package. Subsequently, the Orthologs Group Delineation (OGD) algorithm, an in-house script, is programmatically applied to scan each gene tree. The OGD algorithm is designed to identify OGs and pairwise orthologs directly from the phylogenetic tree. It infers OGs by detecting duplication events using a modified version of the species overlap algorithm. This process defines subfamilies that represent OGs across various taxonomic levels, all while maintaining the tree's inherent hierarchical structure and accommodating potential phylogenetic inconsistencies and artifacts.

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2025-12-16T11:21:33Z

Description

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

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2023-10-18T17:44:17Z

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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2023-11-06T16:06:47Z

Description

SonicParanoid2 sens

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2023-11-01T11:50:27Z

Description

SonicParanoid2 sens g

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2023-11-01T09:43:49Z