From Gene-Scale to Genome-Scale Phylogenetics: the Data Flood In, but the Challenges Remain.- Phylogenomic Analysis by Chromosome Sorting and Painting.- FISH for Mapping Single Copy Genes.- Construction of Radiation Hybrid Panels.- Survey Sequencing and Radiation Hybrid Mapping to Construct Comparative Maps.- Construction of High-Resolution Comparative Maps in Mammals Using BAC-End Sequences.- Amniote Phylogenomics: Testing Evolutionary Hypotheses with BAC Library Scanning and Targeted Clone Analysis of Large-Scale DNA Sequences from Reptiles.- Comparative Physical Mapping: Universal Overgo Hybridization Probe Design and BAC Library Hybridization.- Phylogenomic Resources at the UCSC Genome Browser.- Computational Tools for the Analysis of Rearrangements in Mammalian Genomes.- Computational Reconstruction of Ancestral DNA Sequences.- Sequencing and Phylogenomic Analysis of Whole Mitochondrial Genomes of Animals.- Retroposons: Genetic Footprints on the Evolutionary Paths of Life.- LINE-1 Elements: Analysis by Fluorescence In-Situ Hybridization and Nucleotide Sequences.- Identification of Cryptic Sex Chromosomes and Isolation of X- and Y-Borne Genes.
