TreSpEx-detection of misleading signal in phylogenetic reconstructions based on tree information
Open accessAbstract
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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Resulting gene trees were used with TreSpEx for more thorough screening of paralogs and contamination that may have passed through initial orthology determination.
“Resulting gene trees were used with TreSpEx 56 for more thorough screening of paralogs and contamination that may have passed through initial orthology determination.”
From Ctenophore relationships and their placement as the sister group to all other animals (2017) · cites this paper as [56]
Standard measurements of sequence saturation average across the length of the sequence.
“standard measurements of sequence saturation (7,8,25) average across the length of the sequence.”
From Error, signal, and the placement of Ctenophora sister to all other animals (2015) · cites this paper as [25]
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- Authors
- Struck, T. H.
- Affiliations
- Zoological Research Museum Alexander Koenig (DE)
- Corresponding author
- Struck, Torsten H.
- ORCID
- Struck, Torsten H.
- Venue
- Evolutionary Bioinformatics
- Publisher
- SAGE Publications
- Published
- 2014-01
- Volume
- 10
- Pages
- 51-67
- ISSN
- 1176-9343 (ISSN-L)
- PMC
- PMC3972080
- OpenAlex
- W1980690176
- Semantic Scholar
- 8feb48cd4ac0d0d60ae78651533c9742d9cfcd74
- Cited by
- 128
- References
- 85
- Citations by year
- 2026: 7 · 2025: 7 · 2024: 14 · 2023: 12 · 2022: 15 · 2021: 10 · 2020: 16 · 2019: 9 · 2018: 3 · 2017: 9 · 2016: 10 · 2015: 11 · 2014: 5
- FWCI
- 4.79
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Evolutionary Bioinformatics (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Informationszentrum Lebenswissenschaften (ZB MED) (submittedVersion, cc-by-nc)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National Science Foundation (1036537)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Keywords
- phylogenetic signal detection, paralogy, long-branch attraction, site saturation, patristic distance, phylogenomic analysis, bioinformatics software
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