Prediction of missing sequences and branch lengths in phylogenomic data
Authors:
- 5 January 2016
- journal article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 32 (9) , 1331-1337
Abstract
Motivation: The presence of missing data in large-scale phylogenomic datasets has negative effects on the phylogenetic inference process. One effect that is caused by alignments with missing per-gene or per-partition sequences is that the inferred phylogenies may exhibit extremely long branch lengths. We investigate if statistically predicting missing sequences for organisms by using information from genes/partitions that have data for these organisms alleviates the problem and improves phylogenetic accuracy.Keywords
This publication has 12 references indexed in Scilit:
- The Phylogenetic Likelihood LibrarySystematic Biology, 2014
- Terraces in Phylogenetic Tree SpaceScience, 2011
- Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical DataSystematic Biology, 2011
- Phylogenetic relationships among arecoid palms (Arecaceae: Arecoideae)Annals of Botany, 2011
- Combining Phylogenomics and Fossils in Higher-Level Squamate Reptile Phylogeny: Molecular Data Change the Placement of Fossil TaxaSystematic Biology, 2010
- Single-copy nuclear genes resolve the phylogeny of the holometabolous insectsBMC Biology, 2009
- The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian InferenceSystematic Biology, 2009
- Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed InsectsSystematic Biology, 2006
- Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUpBiochemistry, 1983
- Comparison of phylogenetic treesMathematical Biosciences, 1981