‘Multi-SpaM’: a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees

[1]  R. Graham,et al.  The steiner problem in phylogeny is NP-complete , 1982 .

[2]  Matteo Comin,et al.  Benchmarking of alignment-free sequence comparison methods , 2019, Genome Biology.

[3]  Brian D. Ondov,et al.  Mash: fast genome and metagenome distance estimation using MinHash , 2015, Genome Biology.

[4]  S. Snir,et al.  The Performance of Two Supertree Schemes Compared Using Synthetic and Real Data Quartet Input , 2018, Journal of Molecular Evolution.

[5]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[6]  O Gascuel,et al.  BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. , 1997, Molecular biology and evolution.

[7]  Burkhard Morgenstern,et al.  Estimating evolutionary distances between genomic sequences from spaced-word matches , 2015, Algorithms for Molecular Biology.

[8]  Steven Salzberg,et al.  Mugsy: fast multiple alignment of closely related whole genomes , 2010, Bioinform..

[9]  James M. Hogan,et al.  Alignment-free inference of hierarchical and reticulate phylogenomic relationships , 2017, Briefings Bioinform..

[10]  Satish Rao,et al.  Quartets MaxCut: A Divide and Conquer Quartets Algorithm , 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[11]  W. Fitch.  Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology , 1971 .

[12]  Thomas Wiehe,et al.  Estimating Mutation Distances from Unaligned Genomes , 2009, J. Comput. Biol..

[13]  Laurent Noé,et al.  Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds , 2017, Algorithms for Molecular Biology.

[14]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[15]  Kai Song,et al.  New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing , 2014, Briefings Bioinform..

[16]  Chi Man Tsang,et al.  Efficient Immortalization of Primary Nasopharyngeal Epithelial Cells for EBV Infection Study , 2013, PloS one.

[17]  G. Gonnet,et al.  ALF—A Simulation Framework for Genome Evolution , 2011, Molecular biology and evolution.

[18]  Umberto Ferraro Petrillo,et al.  An effective extension of the applicability of alignment-free biological sequence comparison algorithms with Hadoop , 2017, The Journal of Supercomputing.

[19]  Burkhard Morgenstern,et al.  Fast and accurate phylogeny reconstruction using filtered spaced-word matches , 2017, Bioinform..

[20]  D. Robinson,et al.  Comparison of phylogenetic trees , 1981 .

[21]  Bernhard Haubold,et al.  Alignment-free phylogenetics and population genetics , 2014, Briefings Bioinform..

[22]  Burkhard Morgenstern,et al.  Fast alignment-free sequence comparison using spaced-word frequencies , 2014, Bioinform..

[23]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[24]  Gesine Reinert,et al.  Alignment-Free Sequence Analysis and Applications. , 2018, Annual review of biomedical data science.

[25]  Gaston H. Gonnet,et al.  The Impact of Gene Duplication, Insertion, Deletion, Lateral Gene Transfer and Sequencing Error on Orthology Inference: A Simulation Study , 2013, PloS one.

[26]  Klas Hatje,et al.  Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches , 2014, Nucleic Acids Res..

[27]  Lucian Ilie,et al.  SpEED: fast computation of sensitive spaced seeds , 2011, Bioinform..

[28]  Srinivas Aluru,et al.  A Provably Efficient Algorithm for the k-Mismatch Average Common Substring Problem , 2016, J. Comput. Biol..

[29]  Umberto Ferraro Petrillo,et al.  A new distributed alignment-free approach to compare whole proteomes , 2017, Theor. Comput. Sci..

[30]  Gregory Kucherov,et al.  Evolution of biosequence search algorithms: a brief survey , 2018, Bioinform..

[31]  Silvana Ilie.  Efficient computation of spaced seeds , 2011, BMC Research Notes.

[32]  David Burstein,et al.  The Average Common Substring Approach to Phylogenomic Reconstruction , 2006, J. Comput. Biol..

[33]  Yongchao Liu,et al.  A greedy alignment-free distance estimator for phylogenetic inference , 2015, 2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).

[34]  Matteo Comin,et al.  Efficient computation of spaced seed hashing with block indexing , 2018, BMC Bioinformatics.

[35]  Huiguang Yi,et al.  Co-phylog: an assembly-free phylogenomic approach for closely related organisms , 2010, Nucleic acids research.

[36]  B. Baum.  Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees , 1992 .

[37]  Burkhard Morgenstern,et al.  Phylogeny reconstruction based on the length distribution of k-mismatch common substrings , 2017, Algorithms for Molecular Biology.

[38]  Mark A. Ragan,et al.  Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer , 2016, Scientific Reports.

[39]  Costas S. Iliopoulos,et al.  Longest Common Prefixes with k-Errors and Applications , 2018, SPIRE.

[40]  Burkhard Morgenstern,et al.  Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences , 2019, GigaScience.

[41]  Bernhard Haubold,et al.  andi: Fast and accurate estimation of evolutionary distances between closely related genomes , 2015, Bioinform..

[42]  Vineet Bafna,et al.  Skmer: assembly-free and alignment-free sample identification using genome skims , 2019, Genome Biology.

[43]  Alok Bhattacharya,et al.  Next-Generation Anchor Based Phylogeny (NexABP): Constructing phylogeny from Next-generation sequencing data , 2013, Scientific Reports.

[44]  Satish Rao,et al.  Quartet MaxCut: a fast algorithm for amalgamating quartet trees. , 2012, Molecular phylogenetics and evolution.

[45]  Jonas S. Almeida,et al.  Alignment-free sequence comparison: benefits, applications, and tools , 2017, Genome Biology.

[46]  K. Hatje,et al.  A Phylogenetic Analysis of the Brassicales Clade Based on an Alignment-Free Sequence Comparison Method , 2012, Front. Plant Sci..

[47]  Burkhard Morgenstern,et al.  kmacs: the k-mismatch average common substring approach to alignment-free sequence comparison , 2014, Bioinform..

[48]  Matteo Comin,et al.  Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns , 2014, BMC Bioinformatics.

[49]  Nick V. Grishin,et al.  Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer , 2016, PLoS Comput. Biol..

[50]  M. Ragan,et al.  Matrix representation in reconstructing phylogenetic relationships among the eukaryotes. , 1992, Bio Systems.

[51]  C. Bleidorn,et al.  Comparative genomics provides a timeframe for Wolbachia evolution and exposes a recent biotin synthesis operon transfer , 2016, Nature Microbiology.

[52]  J. Felsenstein.  Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[53]  J. Farris.  Methods for Computing Wagner Trees , 1970 .

[54]  Tamir Tuller,et al.  Maximum Likelihood of Evolutionary Trees Is Hard , 2005, RECOMB.

[55]  Kai Song,et al.  Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads , 2013, J. Comput. Biol..

[56]  M. Steel.  The complexity of reconstructing trees from qualitative characters and subtrees , 1992 .

[57]  Thomas Mailund,et al.  tqDist: a library for computing the quartet and triplet distances between binary or general trees , 2014, Bioinform..

[58]  Burkhard Morgenstern,et al.  rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison , 2015, PLoS Comput. Biol..