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Thus, this is the fixed matrix that we use in the first part.

Refined alignments with scores above 181 (which roughly corresponds to an E-value of 10) are considered significant.

In contrast, out-paralogs are paralogs that diverged a particular speciation event of reference.

To address the need for reliable sources of orthologs, several initiatives have been created for better orthologs prediction Commonly, there are two classes of prediction methods: ] (as opposed to methods with lower sensitivity such as BLAST), confidence intervals explicitly consider estimation uncertainty, and exclusion of paralogs is achieved using sequences in third-party genomes as "witnesses of non-orthology" [].

Two genes that share a common ancestor are defined as homologs, while genes that are similar in sequence without a common origin are termed analogs.

Homologs can be divided into several classes []: orthologs, which originate from a speciation event; paralogs, which originate from gene duplication; and xenologs, which originate from horizontal gene transfer.

Orthologs are valuable in numerous analyses, including reconstruction of species phylogenies, protein function inference, database annotation, and genomic context analysis.

There are several advantages of using protein sequences rather than using DNA sequences.

We build groups of orthologs using a maximum-weight clique algorithm.

A web interface now enables interactive exploration of the predictions [].

The classification of genes according to evolutionary relations is essential for many aspects of comparative and functional genomics.

Evolutionary relations are often described as pairwise relations.

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