Skmer: assembly-free and alignment-free sample identification using genome skims
The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate
and biodiversity changes. The recent genome-skimming approach extends current …
and biodiversity changes. The recent genome-skimming approach extends current …
The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances
S Röhling, A Linne, J Schellhorn, M Hosseini… - Plos one, 2020 - journals.plos.org
We study the number N k 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 …
DNA sequences, as a function of k. We show that the Jukes-Cantor distance between two …
Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences
CA Leimeister, J Schellhorn, S Dörrer, M Gerth… - …, 2019 - academic.oup.com
Word-based or 'alignment-free'sequence comparison has become an active research area
in bioinformatics. While previous word-frequency approaches calculated rough measures of …
in bioinformatics. While previous word-frequency approaches calculated rough measures of …
Mapping sequence to feature vector using numerical representation of codons targeted to amino acids for alignment-free sequence analysis
The phylogenetic analysis based on sequence similarity targeted to real biological taxa is
one of the major challenging tasks. In this paper, we propose a novel alignment-free …
one of the major challenging tasks. In this paper, we propose a novel alignment-free …
Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage
AK Lau, S Dörrer, CA Leimeister, C Bleidorn… - BMC …, 2019 - Springer
Background In many fields of biomedical research, it is important to estimate phylogenetic
distances between taxa based on low-coverage sequencing reads. Major applications are …
distances between taxa based on low-coverage sequencing reads. Major applications are …
'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees
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 …
recent years. These methods are much faster than traditional, alignment-based approaches …
Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points
Motivation Most methods for pairwise and multiple genome alignment use fast local
homology search tools to identify anchor points, ie high-scoring local alignments of the input …
homology search tools to identify anchor points, ie high-scoring local alignments of the input …
Sequence Comparison Without Alignment: The SpaM Approaches
B Morgenstern - Multiple Sequence Alignment: Methods and Protocols, 2021 - Springer
Sequence alignment is at the heart of DNA and protein sequence analysis. For the data
volumes that are nowadays produced by massively parallel sequencing technologies …
volumes that are nowadays produced by massively parallel sequencing technologies …
CD-MAWS: An alignment-free phylogeny estimation method using cosine distance on minimal absent word sets
Multiple sequence alignment has been the traditional and well established approach of
sequence analysis and comparison, though it is time and memory consuming. As the scale …
sequence analysis and comparison, though it is time and memory consuming. As the scale …
Phylogenetics beyond biology
N Retzlaff, PF Stadler - Theory in Biosciences, 2018 - Springer
Evolutionary processes have been described not only in biology but also for a wide range of
human cultural activities including languages and law. In contrast to the evolution of DNA or …
human cultural activities including languages and law. In contrast to the evolution of DNA or …