ArticleBMC evolutionary biology2011
PhyDesign: an online application for profiling phylogenetic informativeness.
Article in BMC evolutionary biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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63 citing papers in PubMed.
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- Complete plastid genome of Iris orchioides and comparative analysis with 19 Iris plastomes.PloS one · 2024Article
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- Effect of Different Types of Sequence Data on Palaeognath Phylogeny.Genome biology and evolution · 2023Article
- Extensive characterization of 28 complete chloroplast genomes ofComputational and structural biotechnology journal · 2023Article
- Plastome evolution in the East Asian lobelias (Lobelioideae) using phylogenomic and comparative analyses.Frontiers in plant science · 2023Article
- Coalescent-based species delimitation in North American pinyon pines using low-copy nuclear genes and plastomes.American journal of botany · 2022Article
- New data on Henneguya postexilis Minchew, 1977, a parasite of channel catfish Ictalurus punctatus, with notes on resolution of molecular markers for myxozoan phylogeny.Systematic parasitology · 2022Article
- The mitochondrial genomes of Tortricidae: nucleotide composition, gene variation and phylogenetic performance.BMC genomics · 2021Article
- Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree.Genome biology and evolution · 2021Article
- Resolving the Early Divergence Pattern of Teleost Fish Using Genome-Scale Data.Genome biology and evolution · 2021Article
- Phylogenetic and Haplotype Network Analyses ofBiology · 2021Article
- Genome-scale phylogenetic analyses confirm Olpidium as the closest living zoosporic fungus to the non-flagellated, terrestrial fungi.Scientific reports · 2021Article
3 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
backgroundThe 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.
resultsHere, we present PhyDesign, a platform-independent online application that implements the Townsend (2007) phylogenetic informativeness analysis, providing a quantitative prediction of the utility of loci to solve specific phylogenetic questions. An easy-to-use interface facilitates uploading of alignments and ultrametric trees to calculate and depict profiles of informativeness over specified time ranges, and provides rankings of locus prioritization for epochs of interest.
conclusionsBy providing these profiles, PhyDesign facilitates locus prioritization increasing the efficiency of sequencing for phylogenetic purposes compared to traditional studies with more laborious and low capacity screening methods, as well as increasing the accuracy of phylogenetic studies. Together with a manual and sample files, the application is freely accessible at http://phydesign.townsend.yale.edu.
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