An index of substitution saturation and its application.

By Xuhua Xia, Z. Xie, Marco Salemi, Lu Chen, Yong Wang. Molecular Phylogenetics and Evolution, 2003

1,476 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/69434067449de067414d9123ac74faf92518abdd

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. Bui Quang Minh
2. A. von Haeseler
3. M. Heidemaa
4. U. Joger
5. M. Wink
6. C. Albrecht
7. R. Schultheiß
8. R. Lawson

In Molecular Biology

1. Bui Quang Minh
2. M. Wink
3. U. Joger
4. A. von Haeseler
5. M. Heidemaa
6. D. Guicking
7. R. Lawson
8. A. Solé-Cava

Citations in the corpus

• As Time Goes by: A Simple Fool's Guide to Molecular Clock Approaches in Invertebrates* (2009, background): “Test for saturation signifi cant? The test of Xia et al. (2003) did not reveal a signifi cant degree of saturation for any of the three data partitions (see section “Time estimation with calibration point” above).”
• Ultrafast Approximation for Phylogenetic Bootstrap (2013, methodology): “This reinforces the observation that one should assess the phylogenetic signals in the data with, for example, the likelihood mapping (Strimmer and von Haeseler 1997) and saturation plots (Van de Peer et al. 2002; Xia et al. 2003) before carrying out an expensive bootstrap analysis.”
• Evolution and phylogeny of the genus Natrix (Serpentes: Colubridae) (2006, methodology): “Testing for saturation was accomplished with the test of Xia et al. (2003) provided in the program package DAMBE v. 4.2.7 (Xia & Xie, 2001).”
• Eurythoe complanata (Polychaeta: Amphinomidae), the ‘cosmopolitan’ fireworm, consists of at least three cryptic species (2010, methodology): “The possibility of saturation in the rate of base substitutions at the COI gene was assessed by the methods of Xia et al. (2003) using the DAMBE program (Xia and Xie 2001).”
• Molecular Evolution of Human Coronavirus Genomes (2016, neutral): “Alternatively, specific indexes have been developed to detect substitution saturation [79]; in the presence of dS saturation, third-codon positions can be removed to obtain reliable phylogenies.”
• SYSTEMATIC STUDIES ON SAWFLIES OF THE GENERA DOLERUS, EMPRIA, AND CALIROA (HYMENOPTERA: TENTHREDINIDAE) (2004, methodology): “The extent of substitutional saturation for different markers was evaluated using an entropy-based index of substitution saturation (Xia et al., 2003) and the saturation diagrams, both implemented in the PC programme DAMBE, version”
• DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution (2013, positive): “The function for assessing substitution saturation (Xia, Xie, Salemi, et al. 2003; Xia and Lemey 2009) has been used in hundreds of publications in phylogenetic research.”