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Gene families in PhyloGenes are pruned versions <link to FAQ section> of PANTHER gene families (pantherdb.org, PMID:30407594 ref). They contain only genes from selected plant genomes and 10 non-plant model organisms <link to list>. Genes from other genomes in the PANTHER build have been removed (pruned) from the PANTHER gene families and gene trees.
A PANTHERÂ gene family contains genes that are related to each other by descent from a common ancestor, as established by statistical sequence similarity, and whose protein sequences can be aligned reliably into a multiple sequence alignment. The UniProt Reference Proteomes (https://www.ebi.ac.uk/reference_proteomes) used in PANTHER family construction contain one representative protein sequence per gene. A gene family is represented as a phylogenetic gene tree that shows how the family evolved by the processes of speciation, gene duplication, and horizontal transfer.
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