TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops

Milne, Iain; Lindner, Dominik; Bayer, Micha; Husmeier, Dirk; McGuire, Gráinne; Marshall, David; Wright, Frank

doi:10.1093/bioinformatics/btn575

Cited by 590 publications

(427 citation statements)

References 11 publications

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“…Bayesian phylogenetic analysis was performed with mrbayes , implemented through topali v2.5, using the best‐fit model based on the BIC (GTR+G) (Milne et al . 2009). Five independent analyses were run for one million generations, with sampling every 100 simulations (30% burn‐in).…”

Section: Methodsmentioning

confidence: 99%

Ecological host fitting of Trypanosoma cruzi TcI in Bolivia: mosaic population structure, hybridization and a role for humans in Andean parasite dispersal

et al. 2015

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An improved understanding of how a parasite species exploits its genetic repertoire to colonize novel hosts and environmental niches is crucial to establish the epidemiological risk associated with emergent pathogenic genotypes. Trypanosoma cruzi, a genetically heterogeneous, multi‐host zoonosis, provides an ideal system to examine the sylvatic diversification of parasitic protozoa. In Bolivia, T. cruzi I, the oldest and most widespread genetic lineage, is pervasive across a range of ecological clines. High‐resolution nuclear (26 loci) and mitochondrial (10 loci) genotyping of 199 contemporaneous sylvatic TcI clones was undertaken to provide insights into the biogeographical basis of T. cruzi evolution. Three distinct sylvatic parasite transmission cycles were identified: one highland population among terrestrial rodent and triatomine species, composed of genetically homogenous strains (A r = 2.95; PA/L = 0.61; DAS = 0.151), and two highly diverse, parasite assemblages circulating among predominantly arboreal mammals and vectors in the lowlands (A r = 3.40 and 3.93; PA/L = 1.12 and 0.60; DAS = 0.425 and 0.311, respectively). Very limited gene flow between neighbouring terrestrial highland and arboreal lowland areas (distance ~220 km; FST = 0.42 and 0.35) but strong connectivity between ecologically similar but geographically disparate terrestrial highland ecotopes (distance >465 km; FST = 0.016–0.084) strongly supports ecological host fitting as the predominant mechanism of parasite diversification. Dissimilar heterozygosity estimates (excess in highlands, deficit in lowlands) and mitochondrial introgression among lowland strains may indicate fundamental differences in mating strategies between populations. Finally, accelerated parasite dissemination between densely populated, highland areas, compared to uninhabited lowland foci, likely reflects passive, long‐range anthroponotic dispersal. The impact of humans on the risk of epizootic Chagas disease transmission in Bolivia is discussed.

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Section: Methodsmentioning

confidence: 99%

Ecological host fitting of Trypanosoma cruzi TcI in Bolivia: mosaic population structure, hybridization and a role for humans in Andean parasite dispersal

et al. 2015

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“…Two separate runs were started for each of four independent chains, three of them heated, and runs were considered to have achieved convergence if effective sample size values were all over 200, the PSRF þ statistic was close to 1, further confirmed by visual inspection of the log-likelihood plots for both runs. For the mtDNA trees, the best fit model of evolution was determined using TOPALI (Milne et al, 2009). The initial assessment of the Marion Island phylogenetic position based on mtDNA was run for 10 000 000 iterations, with the first 25% iterations discarded as burn-in.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Phylogenomics of the killer whale indicates ecotype divergence in sympatry

et al. 2014

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For many highly mobile species, the marine environment presents few obvious barriers to gene flow. Even so, there is considerable diversity within and among species, referred to by some as the 'marine speciation paradox'. The recent and diverse radiation of delphinid cetaceans (dolphins) represents a good example of this. Delphinids are capable of extensive dispersion and yet many show fine-scale genetic differentiation among populations. Proposed mechanisms include the division and isolation of populations based on habitat dependence and resource specializations, and habitat release or changing dispersal corridors during glacial cycles. Here we use a phylogenomic approach to investigate the origin of differentiated sympatric populations of killer whales (Orcinus orca). Killer whales show strong specialization on prey choice in populations of stable matrifocal social groups (ecotypes), associated with genetic and phenotypic differentiation. Our data suggest evolution in sympatry among populations of resource specialists.

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“…Various user groups conduct analyses in web applications such as Morphobank [8] or Morphbank [7], via locally installed interfaces (e.g. Mesquite [21] or Topali [22] a new simple graphical user interface for RAxML [23]). We plan to provide programmatic access to CSG capabilities so individuals using one of these community tools can deploy jobs to the CSG and receive their results within their normal working environment.…”

Section: Simplify Job Submission/results Retrievalmentioning

confidence: 99%

THE FUNGUSTRICHOPHYTON REDELLIISP. NOV. CAUSES SKIN INFECTIONS THAT RESEMBLE WHITE-NOSE SYNDROME OF HIBERNATING BATS

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Minnis

Meteyer

et al. 2015

Journal of Wildlife Diseases

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Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation. As a result, DNA sequence data are readily available or obtainable for a wide spectrum of organisms, thus creating an unprecedented opportunity to explore evolutionary relationships broadly and deeply across the Tree of Life. Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to powerful computational resources. Local laptop or desktop machines are no longer viable for analysis of the larger data sets available today, and progress in the field relies upon access to large, scalable high-performance computing resources. This paper describes development of the CIPRES Science Gateway, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources. Meeting the needs of the community has included developing infrastructure to provide access, working with the community to improve existing community codes, developing infrastructure to insure the portal is scalable to the entire systematics community, and adopting strategies that make the project sustainable by the community. The CIPRES Science Gateway has allowed more than 1800 unique users to run jobs that required 2.5 million Service Units since its release in December 2009. (A Service Unit is a CPUhour at unit priority).

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TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops

Cited by 590 publications

References 11 publications

Ecological host fitting of Trypanosoma cruzi TcI in Bolivia: mosaic population structure, hybridization and a role for humans in Andean parasite dispersal

Ecological host fitting of Trypanosoma cruzi TcI in Bolivia: mosaic population structure, hybridization and a role for humans in Andean parasite dispersal

Phylogenomics of the killer whale indicates ecotype divergence in sympatry

THE FUNGUSTRICHOPHYTON REDELLIISP. NOV. CAUSES SKIN INFECTIONS THAT RESEMBLE WHITE-NOSE SYNDROME OF HIBERNATING BATS

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