Terrace Aware Phylogenomic Inference from Supermatrices

• DOI: 10.48550/arxiv.1411.3480
• Publication Date: 2014-01-01
• Authors: Olga Chernomor; Arndt von Haeseler; Bùi Quang Minh
• Keywords: Supermatrix; Phylogenomics; Tree (set theory); Terrace (agriculture); Sequence (biology)

One approach in phylogenomics to infer the tree of life is based on concatenated multiple sequence alignments from many genes. Unfortunately, resulting so-called supermatrix usually sparse, that is, not every gene available for all species supermatrix. Due missing information a phylogenetic inference, assuming each evolves with its own substitution model, suffers terraces which trees show same likelihood. Here, we propose terrace aware (PTA) data structure efficient inference under partition models. PTA avoids likelihood computations belonging terrace. implemented IQ-TREE software, and leads an 1.7 6-fold speedup real sets compared na\"ive implementation. Speedups are independent sizes but correlate amount data. Thus, well suited phylogenomic analyses. source codes, binaries documentation freely at http://www.cibiv.at/software/iqtree .