The AxML program family for maximum likelihood‐based phylogenetic tree inference

Stamatakis, Alexandros; Ludwig, Thomas; Meier, Harald

doi:10.1002/cpe.817

Cited by 6 publications

(4 citation statements)

References 20 publications

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“…Details of tree construction can be found in figure legends. COII DNA phylogeny was generated with the AxML method (Stamatakis et al ., 2004) whereas FDH protein phylogenies were calculated with the Phylip protein maximum likelihood (PROTML) algorithm (Felsenstein, 1989). The same filter and alignments were employed when additional tree algorithms (Fitch distance, Phylip protein parsimony) were used to infer node robustness (Felsenstein, 1989).…”

Section: Methodsmentioning

confidence: 99%

Genes for selenium dependent and independent formate dehydrogenase in the gut microbial communities of three lower, wood‐feeding termites and a wood‐feeding roach

Zhang¹,

Matson²,

Leadbetter³

2010

Environmental Microbiology

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Summary The bacterial Wood–Ljungdahl pathway for CO2‐reductive acetogenesis is important for the nutritional mutualism occurring between wood‐feeding insects and their hindgut microbiota. A key step in this pathway is the reduction of CO2 to formate, catalysed by the enzyme formate dehydrogenase (FDH). Putative selenocysteine‐ (Sec) and cysteine‐ (Cys) containing paralogues of hydrogenase‐linked FDH (FDHH) have been identified in the termite gut acetogenic spirochete, Treponema primitia, but knowledge of their relevance in the termite gut environment remains limited. In this study, we designed degenerate PCR primers for FDHH genes (fdhF) and assessed fdhF diversity in insect gut bacterial isolates and the gut microbial communities of termites and cockroaches. The insects examined herein represent three wood‐feeding termite families, Termopsidae, Kalotermitidae and Rhinotermitidae (phylogenetically ‘lower’ termite taxa); the wood‐feeding roach family Cryptocercidae (the sister taxon to termites); and the omnivorous roach family Blattidae. Sec and Cys FDHH variants were identified in every wood‐feeding insect but not the omnivorous roach. Of 68 novel alleles obtained from inventories, 66 affiliated phylogenetically with enzymes from T. primitia. These formed two subclades (37 and 29 phylotypes) almost completely comprised of Sec‐containing and Cys‐containing enzymes respectively. A gut cDNA inventory showed transcription of both variants in the termite Zootermopsis nevadensis (family Termopsidae). The gene patterns suggest that FDHH enzymes are important for the CO2‐reductive metabolism of uncultured acetogenic treponemes and imply that the availability of selenium, a trace element, shaped microbial gene content in the last common ancestor of dictyopteran, wood‐feeding insects, and continues to shape it to this day.

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Section: Methodsmentioning

confidence: 99%

Genes for selenium dependent and independent formate dehydrogenase in the gut microbial communities of three lower, wood‐feeding termites and a wood‐feeding roach

Zhang¹,

Matson²,

Leadbetter³

2010

Environmental Microbiology

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“…Phylogenetic trees were calculated with the tree builder function of the ARB-software , using the AxML þ algorithm (Stamatakis et al, 2004). Results displayed as bar plots, line plots or line-scatter plots are expressed as mean and s.d.…”

Section: Mathematical Analysesmentioning

confidence: 99%

Importance of soil organic matter for the diversity of microorganisms involved in the degradation of organic pollutants

et al. 2014

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Many organic pollutants are readily degradable by microorganisms in soil, but the importance of soil organic matter for their transformation by specific microbial taxa is unknown. In this study, sorption and microbial degradation of phenol and 2,4-dichlorophenol (DCP) were characterized in three soil variants, generated by different long-term fertilization regimes. Compared with a non-fertilized control (NIL), a mineral-fertilized NPK variant showed 19% and a farmyard manure treated FYM variant 46% more soil organic carbon (SOC). Phenol sorption declined with overall increasing SOC because of altered affinities to the clay fraction (soil particles o2 mm in diameter). In contrast, DCP sorption correlated positively with particulate soil organic matter (present in the soil particle fractions of 63-2000 lm). Stable isotope probing identified Rhodococcus, Arthrobacter (both Actinobacteria) and Cryptococcus (Basidiomycota) as the main degraders of phenol. Rhodococcus and Cryptococcus were not affected by SOC, but the participation of Arthrobacter declined in NPK and even more in FYM. 14 C-DCP was hardly metabolized in the NIL variant, more efficiently in FYM and most in NPK. In NPK, Burkholderia was the main degrader and in FYM Variovorax. This study demonstrates a strong effect of SOC on the partitioning of organic pollutants to soil particle size fractions and indicates the profound consequences that this process could have for the diversity of bacteria involved in their degradation.

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“…Our framework plays the role of worker for computing the maximum likelihood during the evaluation of the tree topology in current inference algorithms and tools ([ 38 ], Fig. 2).…”

Section: Resultsmentioning

confidence: 99%

Evaluation of properties over phylogenetic trees using stochastic logics

Requeno

Colom

2016

BMC Bioinformatics

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BackgroundModel checking has been recently introduced as an integrated framework for extracting information of the phylogenetic trees using temporal logics as a querying language, an extension of modal logics that imposes restrictions of a boolean formula along a path of events. The phylogenetic tree is considered a transition system modeling the evolution as a sequence of genomic mutations (we understand mutation as different ways that DNA can be changed), while this kind of logics are suitable for traversing it in a strict and exhaustive way. Given a biological property that we desire to inspect over the phylogeny, the verifier returns true if the specification is satisfied or a counterexample that falsifies it. However, this approach has been only considered over qualitative aspects of the phylogeny.ResultsIn this paper, we repair the limitations of the previous framework for including and handling quantitative information such as explicit time or probability. To this end, we apply current probabilistic continuous-time extensions of model checking to phylogenetics. We reinterpret a catalog of qualitative properties in a numerical way, and we also present new properties that couldn’t be analyzed before. For instance, we obtain the likelihood of a tree topology according to a mutation model. As case of study, we analyze several phylogenies in order to obtain the maximum likelihood with the model checking tool PRISM. In addition, we have adapted the software for optimizing the computation of maximum likelihoods.ConclusionsWe have shown that probabilistic model checking is a competitive framework for describing and analyzing quantitative properties over phylogenetic trees. This formalism adds soundness and readability to the definition of models and specifications. Besides, the existence of model checking tools hides the underlying technology, omitting the extension, upgrade, debugging and maintenance of a software tool to the biologists. A set of benchmarks justify the feasibility of our approach.

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The AxML program family for maximum likelihood‐based phylogenetic tree inference

Cited by 6 publications

References 20 publications

Genes for selenium dependent and independent formate dehydrogenase in the gut microbial communities of three lower, wood‐feeding termites and a wood‐feeding roach

Genes for selenium dependent and independent formate dehydrogenase in the gut microbial communities of three lower, wood‐feeding termites and a wood‐feeding roach

Importance of soil organic matter for the diversity of microorganisms involved in the degradation of organic pollutants

Evaluation of properties over phylogenetic trees using stochastic logics

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