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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2023-07-10T15:02:52+00:00

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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2023-07-04T15:59:57+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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2023-10-11T13:43:48+00:00

Description

FastOMA is a scalable software package to infer orthology relationship

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2023-12-05T13:02:47+00:00

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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2023-07-10T15:10:40+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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2023-07-10T15:15:39+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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2023-11-01T11:38:26+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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2023-11-06T14:31:17+00:00

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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2023-07-10T15:45:45+00:00

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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2023-07-10T15:41:25+00:00

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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2023-11-01T16:15:13+00:00

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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2023-12-05T13:08:32+00:00

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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2023-10-04T14:38:08+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 ALL will return all orthologs if more than one

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2023-10-31T11:11:44+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 ALL will return all orthologs if more than one

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2023-10-31T11:06:46+00:00

Description

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

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2023-10-18T17:44:17+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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2023-11-06T16:06:47+00:00

Description

SonicParanoid2 sens

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2023-11-01T11:50:27+00:00

Description

SonicParanoid2 sens g

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2023-11-01T09:43:49+00:00