DAMBE: software package for data analysis in molecular biology and evolution.

By Xuhua Xia, Z. Xie. Journal of Heredity, 2001

2,344 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/336dc5ace3125bd95cccbf7a9ff53beced98584b

How researchers see this paper

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In Genetics

1. M. Heidemaa
2. Xuhua Xia
3. M. Szarowska
4. U. Joger
5. M. Wink
6. R. Lawson
7. S. Blair Hedges
8. C. Albrecht

In Molecular Biology

1. M. Heidemaa
2. Xuhua Xia
3. M. Wink
4. U. Joger
5. M. Szarowska
6. R. Lawson
7. D. Guicking
8. Z. Xie

Citations in the corpus

• Genome Microevolution of Chikungunya Viruses Causing the Indian Ocean Outbreak (2006, neutral): “13 [14].”
• 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 ).”
• The collision of the Indian plate with Asia: molecular evidence for its impact on the phylogeny of freshwater crabs (Brachyura: Potamidae) (2009, methodology): “…for 10 million generations, with trees sampled every 1000 generations (the first 5000 trees were later discarded as ‘burn-in’). dambe (version 4.5.32; Xia & Xie, 2001) software was used for generating saturation plots for the 16S rRNA, and the pairwise distances were plotted against the genetic…”
• 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).”
• Caprine κ-Casein (CSN3) Polymorphism: New Developments in Molecular Knowledge (2005, methodology): “Calculation of isoelectric points ( IP ) of the protein corresponding to the DNA sequences of Capra hircus CSN3 was done with the DAMBE program (Xia and Xie, 2001).”
• 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 4.2.13 (Xia & Xie, 2001).”
• 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).”
• DNA Barcoding of Lepetodrilus Limpets Reveals Cryptic Species (2008, methodology): “DAMBE: Software Package for Data Analysis in Molecular Biology and Evolution.”
• An index of substitution saturation and its application. (2003, methodology): “The forth approach (Steel et al., 1995; Steel et al., 1993) has just been imple- mented in DAMBE (Xia, 2000; Xia and Xie, 2001) with a few extensions.”
• Genetic characterization of Brazilian bovine viral diarrhea virus isolates by partial nucleotide sequencing of the 5'-UTR region (2006, methodology): “The presence of a phylogenetic signal was verified by the saturation in the curve of transition versus transversion calculated by the software DAMBE (Xia & Xie 2001).”
• The evolutionary history of Trichoptera (Insecta): A case of successful adaptation to life in freshwater (2013, methodology): “This saturation could be made negligible by appropriate modelling, but may even then enforce erroneous signal in the analysis (Xia et al ., 2003). POL had the least saturated of all third codon positions, which appeared phylogenetically informative over the whole tree and was therefore retained in t”
• Molecular systematics of racers, whipsnakes and relatives (Reptilia: Colubridae) using mitochondrial and nuclear markers (2004, methodology): “Measuring of substitution saturation has been done using dambe 4.1.15 (Xia 2000, Xia and Xie 2001) for mitochondrial and c-mos sequences, respectively.”
• Genetic relationships of the western Mediterranean painted frogs based on allozymes and mitochondrial markers: evolutionary and taxonomic inferences (Amphibia, Anura, Discoglossidae) (2006, neutral): “4.1.19 (Xia & Xie, 2001).”
• A new frog family (Anura: Terrarana) from South America and an expanded direct-developing clade revealed by molecular phylogeny (2009, positive): “…within codons of the mitochondrial ND1 and cytochrome b genes showed strong evidence of saturation when plots of transitions and transversions vs. genetic distance were made in DAMBE 5.0.25 (Xia & Xie 2001) and were excluded from the alignment to avoid biasing the non-model based analyses.”
• Timing of the population dynamics of bullhead Cottus gobio (Teleostei: Cottidae) during the Pleistocene (2002, background): “In order to test for the presence of saturation in the sequences, we compared the saturation index expected when assuming full saturations with the observed saturation index (DAMBE 4.0.75; Xia & Xie, 2001).”