‘Multi-SpaM’: a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees
暂无分享,去创建一个
Sagi Snir | Burkhard Morgenstern | Christoph Bleidorn | Michael Gerth | Thomas Dencker | Chris-André Leimeister | B. Morgenstern | S. Snir | C. Bleidorn | Michael Gerth | Chris-André Leimeister | Thomas Dencker
[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..