Towards Phylogenomic Reconstruction

Reconstructing phylogenies is one of the primary objectives in evolution studies. Efficient software to reconstruct phylogenies based on isolated genes has existed for decades, yet, phylogenetic reconstructions from whole genomes are only beginning. The diversification of genome sequencing projects has generated thousands of whole genomes making phylogenomic reconstruction a challenging research topic. In this paper, we present an approach for pairwise alignment construction which deploys both nucleotide and locus (a segment of nucleotides) operations to minimize the total edit cost between genomes. The cost is composed of three factors: nucleotide transformation costs between loci, indel costs of loci, and rearrangement costs between locus orders. This approach is embedded within a direct optimization scheme to reconstruct phylogenies from whole unaligned genomes. Performance of this approach is demonstrated in our software, POY4, to reconstruct phylogenies from Coronavirus and Poxv...

• Type: Conference
• Year: 2007
• Where: BIOCOMP
• Authors: Le Vinh, Andres Varon, Daniel Janies, Ward Wheeler
• Keywords: BIOCOMP 2007, Bioinformatics, Genome Sequencing Projects, Genomes, Phylogenies