ArticleEvolutionary bioinformatics online2014
TreSpEx-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information.
Article in Evolutionary bioinformatics online, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
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- Genomic and ecological drivers of parallel arid adaptation in tree grapes (Vitaceae).Nature communications · 2026Article
- A taxon-rich and genome-scale phylogeny of Opisthokonta.PLoS biology · 2024Article
- The mitochondrial genome of Bottapotamon fukienense (Brachiura: Potamidae) is fragmented into two chromosomes.BMC genomics · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- Distinct hybridization modes in wide- and narrow-ranged lineages of Causonis (Vitaceae).BMC biology · 2023Article
- Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae.Nature communications · 2023Article
- Mitochondrial Genome Evolution in Annelida-A Systematic Study on Conservative and Variable Gene Orders and the Factors Influencing its Evolution.Systematic biology · 2023Article
- Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling.Molecular biology and evolution · 2023Review
- Nano-Strainer: A workflow for the identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads.Ecology and evolution · 2023Article
- Identifying and addressing methodological incongruence in phylogenomics: A review.Evolutionary applications · 2023Review
- A global phylogenomic analysis of the shiitake genusProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Mitochondrial phylogenomics provides conclusive evidence that the family Ancyrocephalidae is deeply paraphyletic.Parasites & vectors · 2023Article
- Article
- Insights from the genomes of 4 diploid Camelina spp.G3 (Bethesda, Md.) · 2022Article
- Different phylogenomic methods support monophyly of enigmatic 'Mesozoa' (Dicyemida + Orthonectida, Lophotrochozoa).Proceedings. Biological sciences · 2022Article
- Phylotranscriptomics Resolves the Phylogeny of Pooideae and Uncovers Factors for Their Adaptive Evolution.Molecular biology and evolution · 2022Article
- Plastid phylogenomics of tribe Perseeae (Lauraceae) yields insights into the evolution of East Asian subtropical evergreen broad-leaved forests.BMC plant biology · 2022Article
- Quantitative Insights into the Contribution of Nematocysts to the Adaptive Success of Cnidarians Based on Proteomic Analysis.Biology · 2022Article
Corrections and comments
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Abstract
Phylogenies of species or genes are commonplace nowadays in many areas of comparative biological studies. However, for phylogenetic reconstructions one must refer to artificial signals such as paralogy, long-branch attraction, saturation, or conflict between different datasets. These signals might eventually mislead the reconstruction even in phylogenomic studies employing hundreds of genes. Unfortunately, there has been no program allowing the detection of such effects in combination with an implementation into automatic process pipelines. TreSpEx (Tree Space Explorer) now combines different approaches (including statistical tests), which utilize tree-based information like nodal support or patristic distances (PDs) to identify misleading signals. The program enables the parallel analysis of hundreds of trees and/or predefined gene partitions, and being command-line driven, it can be integrated into automatic process pipelines. TreSpEx is implemented in Perl and supported on Linux, Mac OS X, and MS Windows. Source code, binaries, and additional material are freely available at http://www.annelida.de/research/bioinformatics/software.html.
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