This study focuses on detecting nonneutral substitution rates in mammalian phylogenies, aiming to identify candidate functional elements. Four statistical phylogenetic tests—likelihood ratio (LRT), score, exact distribution-based, and genomic evolutionary rate profiling (GERP)—are compared for their ability to detect both conservation and acceleration in genomic elements. These tests are implemented in the phyloP program, which is freely available. Extensive simulation experiments show that all four methods have similar statistical power, with good sensitivity for detecting strong selection at individual nucleotides, moderate selection in 3-bp elements, and weaker or clade-specific selection in longer elements. Applying phyloP to multiple alignments from the ENCODE project, the authors analyze patterns of conservation and acceleration in known and predicted functional elements, estimate fractions of sites under constraint, and examine clade-specific selection differences in primates and glires. New "Conservation" tracks in the UCSC Genome Browser display phyloP and phastCons scores for genome-wide alignments of 44 vertebrate species. The study highlights the effectiveness of these methods in identifying functional elements and provides a valuable resource for comparative genomics research.This study focuses on detecting nonneutral substitution rates in mammalian phylogenies, aiming to identify candidate functional elements. Four statistical phylogenetic tests—likelihood ratio (LRT), score, exact distribution-based, and genomic evolutionary rate profiling (GERP)—are compared for their ability to detect both conservation and acceleration in genomic elements. These tests are implemented in the phyloP program, which is freely available. Extensive simulation experiments show that all four methods have similar statistical power, with good sensitivity for detecting strong selection at individual nucleotides, moderate selection in 3-bp elements, and weaker or clade-specific selection in longer elements. Applying phyloP to multiple alignments from the ENCODE project, the authors analyze patterns of conservation and acceleration in known and predicted functional elements, estimate fractions of sites under constraint, and examine clade-specific selection differences in primates and glires. New "Conservation" tracks in the UCSC Genome Browser display phyloP and phastCons scores for genome-wide alignments of 44 vertebrate species. The study highlights the effectiveness of these methods in identifying functional elements and provides a valuable resource for comparative genomics research.