Most of the alignment-free algorithms reviewed were implemented in MATLAB code and are available at http://bioinformatics.musc.edu/resources.html

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis. However, many researchers are unclear about how these methods work, how they compare to alignment-based methods, and what their potential is for use for their research. We address these questions and provide a guide to the currently available alignment-free sequence analysis tools.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1319-7) contains supplementary material, which is available to authorized users.

A preliminary Web-based application for ANN smoothing is accessible at http://bioinformatics.musc.edu/webmetabol/. S-systems can be interactively analyzed with the user-friendly freeware PLAS (http://correio.cc.fc.ul.pt/~aenf/plas.html) or with the MATLAB module BSTLab (http://bioinformatics.musc.edu/bstlab/), which is currently being beta-tested.

The studies that correlate the results obtained by different typing methodologies rely solely on qualitative comparisons of the groups defined by each methodology. We propose a framework of measures for the quantitative assessment of correspondences between different typing methods as a first step to the global mapping of type equivalences. A collection of 325 macrolide-resistant Streptococcus pyogenes isolates associated with pharyngitis cases in Portugal was used to benchmark the proposed measures. All isolates were characterized by macrolide resistance phenotyping, T serotyping, emm sequence typing, and pulsed-field gel electrophoresis (PFGE), using SmaI or Cfr9I and SfiI. A subset of 41 isolates, representing each PFGE cluster, was also characterized by multilocus sequence typing (MLST). The application of Adjusted Rand and Wallace indices allowed the evaluation of the strength and the directionality of the correspondences between the various typing methods and showed that if PFGE or MLST data are available one can confidently predict the emm type (Wallace coefficients of 0.952 for both methods). In contrast, emm typing was a poor predictor of PFGE cluster or MLST sequence type (Wallace coefficients of 0.803 and 0.655, respectively). This was confirmed by the analysis of the larger data set available from http://spyogenes.mlst.net and underscores the necessity of performing PFGE or MLST to unambiguously define clones in S. pyogenes.Typing methods are major tools for the epidemiological characterization of bacterial pathogens, allowing the determination of the clonal relationships between isolates based on their genotypic or phenotypic characteristics. Recent technological advances have resulted in a shift from classical phenotypic typing methods, such as serotyping, biotyping, and antibiotic resistance typing, to molecular methods such as restriction fragment length polymorphism (8), pulsed-field gel electrophoresis (PFGE) (25), and PCR serotyping (4). With the availability of affordable sequencing methods, another shift occurred towards sequence-based typing methods such as multilocus sequence typing (MLST) (18) and emm sequence typing (2). Sequence-based methods have a wide appeal since they provide unambiguous data and are intrinsically portable, allowing the creation of databases that, if publicly available through the internet, enable the comparison of local data with those of previous studies in different geographical locations. Ideally, an analysis of each typing method, in terms of discriminatory power, reproducibility, typeability, feasibility, and other characteristics as suggested by Struelens (31), should be performed to better determine which method is appropriate in a given setting.Several molecular epidemiology studies of clinically relevant microorganisms provide a characterization of isolates based on different typing methods (6,8,20,23). Frequently these studies focus on a comparison between the assigned types of different typing methods, from a qualitative point of view, i.e., indicating c...