PhyDesign: an online application for profiling phylogenetic informativeness
Open Access
- 31 May 2011
- journal article
- Published by Springer Nature in BMC Ecology and Evolution
- Vol. 11 (1) , 152
Abstract
The rapid increase in number of sequenced genomes for species across of the tree of life is revealing a diverse suite of orthologous genes that could potentially be employed to inform molecular phylogenetic studies that encompass broader taxonomic sampling. Optimal usage of this diversity of loci requires user-friendly tools to facilitate widespread cost-effective locus prioritization for phylogenetic sampling. The Townsend (2007) phylogenetic informativeness provides a unique empirical metric for guiding marker selection. However, no software or automated methodology to evaluate sequence alignments and estimate the phylogenetic informativeness metric has been available.Keywords
This publication has 16 references indexed in Scilit:
- Taxon Sampling and the Optimal Rates of Evolution for Phylogenetic InferenceSystematic Biology, 2011
- UniPrime2: a web service providing easier Universal Primer designNucleic Acids Research, 2009
- FUNYBASE: a FUNgal phYlogenomic dataBASEBMC Bioinformatics, 2008
- The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate TreeJournal of Molecular Evolution, 2008
- Utility of arginine kinase for resolution of phylogenetic relationships among brachyuran genera and familiesMolecular Phylogenetics and Evolution, 2008
- Profiling Phylogenetic InformativenessSystematic Biology, 2007
- OrthoMaM: A database of orthologous genomic markers for placental mammal phylogeneticsBMC Ecology and Evolution, 2007
- HyPhy: hypothesis testing using phylogeniesBioinformatics, 2004
- Comparison of Site-Specific Rate-Inference Methods for Protein Sequences: Empirical Bayesian Methods Are SuperiorMolecular Biology and Evolution, 2004
- The Bioperl Toolkit: Perl Modules for the Life SciencesGenome Research, 2002