Comparison of alignment free string distances for complete genome phylogeny

DOI10.1007/S11634-009-0041-ZMaRDI QIDQ2442771zbMATH OpenOpenAlexFDO

Authors Frédéric Guyon, Céline Brochier-Armanet, Alain Guénoche

Publication date 1 April 2014

Published in Advances in Data Analysis and Classification. ADAC (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s11634-009-0041-z

zbMATH Keywords

complete bacterial genomesphylogenystring distances

Mathematics Subject Classification ID

Trees (05C05) Combinatorics on words (68R15) Combinatorial optimization (90C27) Taxonomy, cladistics, statistics in mathematical biology (92B10) Protein sequences, DNA sequences (92D20)

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Cites work

• A universal algorithm for sequential data compression
• An Evolutionary Distance Based on Maximal Unique Matches
• Comparison of phylogenetic trees
• scientific article; zbMATH DE number 3736679 (Why is no real title available?)
• Maximum Agreement Subtree in a Set of Evolutionary Trees: Metrics and Efficient Algorithms
• PROKARYOTIC PHYLOGENY BASED ON COMPLETE GENOMES WITHOUT SEQUENCE ALIGNMENT

Cited in

(8)

• Viral genome phylogeny based on Lempel-Ziv complexity and Hausdorff distance
• Alignment free comparison: similarity distribution between the DNA primary sequences based on the shortest absent word
• PROKARYOTIC PHYLOGENY BASED ON COMPLETE GENOMES WITHOUT SEQUENCE ALIGNMENT
• A low-complexity distance for DNA strings
• Efficient Enumeration of Phylogenetically Informative Substrings
• Parametric analysis of alignment and phylogenetic uncertainty
• Research in Computational Molecular Biology
• Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis

Describes a project that uses

Uses Software

• MUMMER
• MUSCLE

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