TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments

Milne, Iain; Wright, Frank; Rowe, Glenn; Marshall, David; Husmeier, Dirk; McGuire, Gráinne

doi:10.1093/bioinformatics/bth155

Cited by 354 publications

(236 citation statements)

References 6 publications

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“…Putative recombination breakpoints within gene segments were calculated from aligned single gene segment sequences using the TOPALi software (http:/ /www.bioss.ac.uk/knowledge/ topali/) (Milne et al 2004) with the difference of squares (DSS) option. The statistical significance of DSS peaks, determined by the f test (Bruen et al 2006) within the TOPALi package, was estimated with parametric bootstrapping.…”

Section: Methodsmentioning

confidence: 99%

“…To test whether intragenic recombination could be detected in any of these sequences, individual gene segment alignments were analyzed by the TOPALi package, which searches for statistically significant evidence of chimeric sequences in aligned sequences (Milne et al 2004). This analysis revealed 9 of the 39 gene segments that show such evidence for recombination (Pis_Gen_8,Pis_Gen_12,Pis_Gen_28,Psat_EST_163,Psat_EST_178,Psat_EST_190,Psat_ EST_191,Psat_EST_196,and Psat_EST_202;supplemental Figure 3 at http:/ /www.genetics.org/supplemental/).…”

Section: Diversity Genetic Linkage and Linkage Disequilibriummentioning

confidence: 99%

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Gene-Based Sequence Diversity Analysis of Field Pea (Pisum)

et al. 2007

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Sequence diversity of 39 dispersed gene loci was analyzed in 48 diverse individuals representative of the genus Pisum. The different genes show large variation in diversity parameters, suggesting widely differing levels of selection and a high overall diversity level for the species. The data set yields a genetic diversity tree whose deep branches, involving wild samples, are preserved in a tree derived from a polymorphic retrotransposon insertions in an identical sample set. Thus, gene regions and intergenic ''junk DNA'' share a consistent picture for the genomic diversity of Pisum, despite low linkage disequilibrium in wild and landrace germplasm, which might be expected to allow independent evolution of these very different DNA classes. Additional lines of evidence indicate that recombination has shuffled gene haplotypes efficiently within Pisum, despite its high level of inbreeding and widespread geographic distribution. Trees derived from individual gene loci show marked differences from each other, and genetic distance values between sample pairs show high standard deviations. Sequence mosaic analysis of aligned sequences identifies nine loci showing evidence for intragenic recombination. Lastly, phylogenetic network analysis confirms the non-treelike structure of Pisum diversity and indicates the major germplasm classes involved. Overall, these data emphasize the artificiality of simple tree structures for representing genomic sequence variation within Pisum and emphasize the need for fine structure haplotype analysis to accurately define the genetic structure of the species.T HE genetic diversity of a species is the sum of its total DNA sequence variation, resulting from millions of years of cumulative mutation, recombination, and selection. Understanding the pattern of the diversity within cultivated plant species and their wild relatives is both interesting and practically important from the viewpoint of conservation and use. Therefore, the ways by which genetic diversity in populations are estimated and represented are important. A popular approach for measuring the genetic diversity of accessions of a species is to analyze samples from gene banks (germplasm collections) by one or more of the many available molecular marker methods. The effectiveness of this strategy depends upon the suitability of the marker method for analyzing the diversity of the sample collection under investigation. Different marker methods can give different views of diversity, depending upon the evolutionary parameters of the underlying DNA sequence variation. Rapidly evolving DNAs, such as simple sequence repeats (SSRs), give high resolution views of relatedness; single nucleotide polymorphism (SNP)-based variation is more suited to deeper relationships, reflecting the slow mutation rate for this type of sequence variation; and transposon insertion-based marker methods should lie between these two, reflecting their intermediate mutation rate, although few studies have been carried out to test this. Furthermore, the g...

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Section: Methodsmentioning

confidence: 99%

Section: Diversity Genetic Linkage and Linkage Disequilibriummentioning

confidence: 99%

Gene-Based Sequence Diversity Analysis of Field Pea (Pisum)

et al. 2007

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“…Prior to phylogenetic analyses, the best-fitting evolutionary model was selected independently for each partition using Modeltest 3.7 (Posada and Crandall, 1998) and the Model Selection option from Topali v2.5 (Milne et al, 2004). A GTR + I + G model was selected for all three markers.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Phylogenetic relationships and evolution of pulmonate gastropods (Mollusca): New insights from increased taxon sampling

Dayrat

Conrad

Balayan

et al. 2011

Molecular Phylogenetics and Evolution

142

182

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“…Trees were replicated 100 times to provide bootstrap support for clades. The analysis was performed using Topali v2.5 software 16 . Eleven published HBoV sequences within the NP-1 region were obtained from the GenBank database (NCBI).…”

Section: Populationmentioning

confidence: 99%

Frequency of human bocavirus respiratory infections among at-risk patients in São Paulo, Brazil

Caccia

Watanabe

Carraro³

et al. 2012

Rev. Inst. Med. trop. S. Paulo

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SUMMARYBackground and objectives: Human Bocavirus (HBoV) has been described since 2005 as an etiological agent of respiratory virus infections. From 2001 to 2008 we investigated the etiology of HBoV among adults and children in different groups at risk of presenting complications arising from acute respiratory infection, the investigation was carried out in a tertiary hospital health care system in Brazil. Methods: HBoV DNA was assayed in 598 respiratory samples from community and hospitalized patients by PCR.Results: Of the 598 tested samples, 2.44% (8/328) of children, including five children with heart disease, and 0.4% (1/270) of adult bone-marrow-transplant were HBoV positive. Conclusions: These data suggested lower HBoV frequency among different at-risk patients and highlights the need to better understand the real role of HBoV among acute respiratory symptomatic patients.

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TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments

Abstract: TOPALi is freely available from http://www.bioss.ac.uk/software.html

Cited by 354 publications

References 6 publications

Gene-Based Sequence Diversity Analysis of Field Pea (Pisum)

Gene-Based Sequence Diversity Analysis of Field Pea (Pisum)

Phylogenetic relationships and evolution of pulmonate gastropods (Mollusca): New insights from increased taxon sampling

Frequency of human bocavirus respiratory infections among at-risk patients in São Paulo, Brazil

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