Paralogous genes (or paralogs) are a particular class of homologous genes. They are the result of gene duplication and the gene copies resulting from the duplication are called paralogous of each other. After duplication, the paralogous genes can keep the same function (for example, the multiple copies of ribosomal RNA genes found in many genomes), but they often diverge and develop different functions (for example, the translation elongation factors Tu and G). Paralogous genes can be retained in the genome after their duplication, but some copies can also be lost. This can generate complex patterns of presence/absence of the different paralogues that may render very difficult the interpretation of phylogenetic trees, leading sometimes to erroneous inferences about the relationships between species. This is usually called the “hidden paralogy” problem.