An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data

摘要: Next-generation sequencing technologies are rapidly generating whole-genome datasets for an increasing number of organisms. However, phylogenetic reconstruction genomic data remains difficult because de novo assembly non-model genomes and multi-genome alignment challenging. To greatly simplify the analysis, we present Assembly Alignment-Free (AAF) method ( https://sourceforge.net/projects/aaf-phylogeny ) that constructs phylogenies directly from unassembled genome sequence data, bypassing both alignment. Using mathematical calculations, models evolution, simulated published genomes, address evolutionary sampling issues caused by direct reconstruction, including homoplasy, errors, incomplete coverage. From these results, calculate statistical properties pairwise distances between allowing us to optimize parameter selection perform bootstrapping. As a test case with real successfully reconstructed phylogeny 12 mammals using raw reads. We also applied AAF 21 tropical tree low coverage demonstrate its effectiveness on Our opens up phylogenomics species without appropriate reference or high coverage, creates framework further analysis structure diversity among