Thomas Dencker
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View article: Insertions and deletions as phylogenetic signal in an alignment-free context
Insertions and deletions as phylogenetic signal in an alignment-free context Open
Most methods for phylogenetic tree reconstruction are based on sequence alignments; they infer phylogenies from substitutions that may have occurred at the aligned sequence positions. Gaps in alignments are usually not employed as phylogen…
View article: The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances
The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances Open
We study the number Nk of length-k word matches between pairs of evolutionarily related DNA sequences, as a function of k. We show that the Jukes-Cantor distance between two genome sequences-i.e. the number of substitutions per site that o…
View article: Alignment-free Phylogeny Reconstruction Based On Quartet Trees
Alignment-free Phylogeny Reconstruction Based On Quartet Trees Open
Traditional methods for phylogeny reconstruction are based on multiple sequence alignments and character-based methods. This combination of computationally expensive methods leads to very accurate results, but it is ill-suited to handle th…
View article: ‘Multi-SpaM’: a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees
‘Multi-SpaM’: a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees Open
Word-based or ‘alignment-free’ methods for phylogeny inference have become popular in recent years. These methods are much faster than traditional, alignment-based approaches, but they are generally less accurate. Most alignment-free metho…
View article: Benchmarking of alignment-free sequence comparison methods
Benchmarking of alignment-free sequence comparison methods Open
Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers t…
View article: Additional file 1: of Benchmarking of alignment-free sequence comparison methods
Additional file 1: of Benchmarking of alignment-free sequence comparison methods Open
Parameter values and detailed benchmarking results of alignment-free tools included in this study. (XLSX 82 kb)
View article: Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points
Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points Open
Motivation Most methods for pairwise and multiple genome alignment use fast local homology search tools to identify anchor points, i.e. high-scoring local alignments of the input sequences. Sequence segments between those anchor points are…
View article: Multi-SpaM: a Maximum-Likelihood approach to Phylogeny reconstruction based on Multiple Spaced-Word Matches
Multi-SpaM: a Maximum-Likelihood approach to Phylogeny reconstruction based on Multiple Spaced-Word Matches Open
Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input sequen…
View article: Multi-SpaM: A Maximum-Likelihood Approach to Phylogeny Reconstruction Using Multiple Spaced-Word Matches and Quartet Trees
Multi-SpaM: A Maximum-Likelihood Approach to Phylogeny Reconstruction Using Multiple Spaced-Word Matches and Quartet Trees Open
Word-based or ‘alignment-free’ methods for phylogeny reconstruction are much faster than traditional, alignment-based approaches, but they are generally less accurate. Most alignment-free methods calculate pairwise distances for a set of i…
View article: Anchor points for genome alignment based on Filtered Spaced Word Matches
Anchor points for genome alignment based on Filtered Spaced Word Matches Open
Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as {\em anchor points} to reduce the search space of the alignment procedure.…