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Fast algorithms for computing sequence distances by exhaustive substring composition.

Apostolico A, Denas O.

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The average common substring approach to phylogenomic reconstruction.

Ulitsky I, Burstein D, Tuller T, Chor B.

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An improved string composition method for sequence comparison.

Lu G, Zhang S, Fang X.

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A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions.

Bader M, Abouelhoda MI, Ohlebusch E.

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The position end-set tree: a small automaton for word recognition in biological sequences.

Lefèvre C, Ikeda JE.

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Local decoding of sequences and alignment-free comparison.

Didier G, Laprevotte I, Pupin M, Hénaut A.

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Improved algorithms for approximate string matching (extended abstract).

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Maximum similarity: a new formulation of phylogenetic reconstruction.

Huang X, Vingron M.

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Non-similarity combinatorial problems.

Rubinov AR, Timkovsky VG.

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Estimating mutation distances from unaligned genomes.

Haubold B, Pfaffelhuber P, Domazet-Loso M, Wiehe T.

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Fast and accurate multi-class protein fold recognition with spatial sample kernels.

Kuksa P, Huang PH, Pavlovic V.

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Microarrays and high-throughput transcriptomic analysis in species with incomplete availability of genomic sequences.

Pariset L, Chillemi G, Bongiorni S, Romano Spica V, Valentini A.

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Pattern-based phylogenetic distance estimation and tree reconstruction.

Höhl M, Rigoutsos I, Ragan MA.

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ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets.

Lin GN, Cai Z, Lin G, Chakraborty S, Xu D.

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Phylogenetic inference with weighted codon evolutionary distances.

Criscuolo A, Michel CJ.

J Mol Evol. 2009 Apr;68(4):377-92. Epub 2009 Mar 24.PMID: 19308635 [PubMed - indexed for MEDLINE]Related articles

Triplet supertree heuristics for the tree of life.

Lin HT, Burleigh JG, Eulenstein O.

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A novel method to analyze the similarity of biological sequences.

Huang W, Guo Y, Zhang J.

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Transition state-finding strategies for use with the growing string method.

Goodrow A, Bell AT, Head-Gordon M.

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Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches.

Cheung F, Win J, Lang JM, Hamilton J, Vuong H, Leach JE, Kamoun S, André Lévesque C, Tisserat N, Buell CR.

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Time warp edit distance with stiffness adjustment for time series matching.

Marteau PF.

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