Public Projects 2020




Domainoid+



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.
Predictions
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2021-05-27T12:52:29+00:00

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
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2021-05-27T12:51:55+00:00

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
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2021-05-27T12:53:02+00:00

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
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2021-05-27T12:47:31+00:00

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
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2021-05-27T12:49:07+00:00

OrthoFinder-2.5.2-MSA



Description
OrthoFinder 2.5.2 using BLAST and multiple sequence alignment tree.Command: "orthofinder -S blast -f -M msa 2011_04_reference_proteomes/"
Predictions
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2021-05-27T12:49:54+00:00

PANTHER 16.0 (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 LDO will return only least diverged ortholog for each gene (single best ortholog)
Predictions
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2021-05-27T12:51:10+00:00

PANTHER 16.0 (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
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2021-05-27T12:50:39+00:00

SonicParanoid



Description
version: 1.0.9 mode: sensitive Length difference threshold = 0.5
Predictions
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2021-05-27T12:57:25+00:00

SonicParanoid_fast



Description
version: 1.0.9 mode: sensitive Length difference threshold = 0.5
Predictions
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2021-05-27T12:58:45+00:00

SonicParanoid_most-sensitive



Description
version 1.2.6
Predictions
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2021-05-27T12:53:57+00:00

SonicParanoid_sensitive



Description
version: 1.0.9 mode: sensitive Length difference threshold = 0.5
Predictions
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2021-05-27T12:56:42+00:00