Alignment-free sequence comparison: benefits, applications, and tools

Zieleziński, Andrzej; Vinga, Susana; Almeida, Jonas S.; Karłowski, Wojciech M.

doi:10.1186/s13059-017-1319-7

Cited by 442 publications

(477 citation statements)

References 183 publications

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“…Another alternative is UPGMA, though as a hierarchical clustering method it would not be expected to recover the same topology as a phylogenetic method (but perhaps the same clusters). However, in the present era, we see the main advantage of this class of methods as being able to avoid having to create an alignment from mapping 49 . If one is able to calculate genetic distances from assemblies or even directly from reads, the relatively costly and challenging step of creating a large multiple sequence alignment can be avoided.…”

Section: Resultsmentioning

confidence: 99%

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Lees¹,

Kendall²,

Parkhill³

et al. 2018

Wellcome Open Res

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Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined “true tree” using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons.

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Section: Resultsmentioning

confidence: 99%

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Lees¹,

Kendall²,

Parkhill³

et al. 2018

Wellcome Open Res

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“…The short length and low sequence identity of defensin sequences can make them challenging to study using traditional methods such as phylogenetics . Repeated mutation at the same location can obscure phylogenetic relationships by saturation effects and long branch attraction .…”

Section: Introductionmentioning

confidence: 99%

“…[16][17][18] The short length and low sequence identity of defensin sequences can make them challenging to study using traditional methods such as phylogenetics. 19 Repeated mutation at the same location can obscure phylogenetic relationships by saturation effects and long branch attraction. 20 It has not been possible to resolve the phylogeny of the whole superfamily; although, smaller phylogenies of the α-, βand big-defensin families have been published previously.…”

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confidence: 99%

Evolution of cnidarian trans‐defensins: Sequence, structure and exploration of chemical space

et al. 2019

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Many of the small, cysteine‐rich ion‐channel modulatory peptides found in Cnidaria are distantly related to vertebrate defensins (of the trans‐defensin superfamily). Transcriptomic and proteomic studies of the endemic Australian speckled sea anemone (Oulactis sp.) yielded homologous peptides to known defensin sequences. We extended these data using existing and custom‐built hidden Markov models to extract defensin‐like families from the transcriptomes of seven endemic Australian cnidarian species. Newly sequenced transcriptomes include three species of Actiniaria (true sea anemones); the speckled anemone (Oulactis sp.), Oulactis muscosa, Dofleinia cf. armata and a species of Corallimorpharia, Rhodactis sp. We analyzed these novel defensin‐like sequences along with published homologues to study the evolution of their physico‐chemical properties in vertebrate and invertebrate fauna. The cnidarian trans‐defensins form a distinct cluster within the chemical space of the superfamily, with a unique set of motifs and biophysical properties. This cluster contains identifiable subgroups, whose distribution in chemical space also correlates with the divergent evolution of their structures. These sequences, currently restricted to cnidarians, form an evolutionarily distinct clade within the trans‐defensin superfamily.

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“…They first identify homologous regions between two genomes, at either the DNA or protein level, and then use these alignments to build phylogenetic trees to infer relationships (Konstantinidis and Tiedje, 2005) (Parks et al, 2018). This approach has several limitations, including low sensitivity to detect remotely related species, slow computing, and low scalability (reviewed in (Zielezinski et al, 2017)). To overcome these limitations, several alignment-free methods were developed that are both computationally efficient and resistant to noise (Zielezinski et al, 2017;Ren et al, 2018;Jain et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

“…This approach has several limitations, including low sensitivity to detect remotely related species, slow computing, and low scalability (reviewed in (Zielezinski et al, 2017)). To overcome these limitations, several alignment-free methods were developed that are both computationally efficient and resistant to noise (Zielezinski et al, 2017;Ren et al, 2018;Jain et al, 2018). Based on their methodologies, there are three main categories of alignment-free genome similarity comparisons (reviewed in (Zielezinski et al, 2017)).…”

Section: Introductionmentioning

confidence: 99%

A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome

Zhong

Egan

et al. 2019

Preprint

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Classifying taxa, including those that have not previously been identified, is a key task in characterizing the microbial communities of under-described habitats, including permanently ice-covered lakes in the dry valleys of the Antarctic. Current supervised phylogeny-based methods fall short on recognizing species assembled from metagenomic datasets from such habitats, as they are often incomplete or lack closely known relatives. Here, we report an efficient software suite, "Genome Constellation", that is capable of rapidly characterizing a large number of metagenome-assembled genomes. Genome Constellation estimates similarities between genomes based on their k-mer matches, and subsequently uses these similarities for classification, clustering, and visualization. The clusters of reference genomes formed by Genome Constellation closely resemble known phylogenetic relationships while simultaneously revealing unexpected connections. In a dataset containing 1,693 draft genomes assembled from the Antarctic lake communities where only 40% could be placed in a phylogenetic tree, Genome Constellation improves taxa assignment to 61%. The clustering-based analysis revealed several novel taxa groups, including six clusters that may represent new bacterial phyla. Remarkably, we discovered 63 new giant viruses, 3 of which could not be found by using the traditional marker-based approach. In summary, we demonstrate that Genome Constellation provides an unbiased option to rapidly analyze a large number of microbial genomes and visually explore their relatedness. The software is available under BSD license at: https://bitbucket.org/berkeleylab/jgi-genomeconstellation/.

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Alignment-free sequence comparison: benefits, applications, and tools

Cited by 442 publications

References 183 publications

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Evolution of cnidarian trans‐defensins: Sequence, structure and exploration of chemical space

A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome

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