Fast and accurate phylogeny reconstruction using filtered spaced-word matches
CA Leimeister, S Sohrabi-Jahromi… - …, 2017 - academic.oup.com
Motivation Word-based or 'alignment-free'algorithms are increasingly used for phylogeny
reconstruction and genome comparison, since they are much faster than traditional …
reconstruction and genome comparison, since they are much faster than traditional …
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 …
Minimally overlapping words for sequence similarity search
Motivation Analysis of genetic sequences is usually based on finding similar parts of
sequences, eg DNA reads and/or genomes. For big data, this is typically done via 'seeds' …
sequences, eg DNA reads and/or genomes. For big data, this is typically done via 'seeds' …
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 …
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 …
Mismatch-tolerant, alignment-free sequence classification using multiple spaced seeds and multiindex Bloom filters
Alignment-free classification tools have enabled high-throughput processing of sequencing
data in many bioinformatics analysis pipelines primarily due to their computational …
data in many bioinformatics analysis pipelines primarily due to their computational …
Fast gapped k-mer counting with subdivided multi-way bucketed cuckoo hash tables
J Zentgraf, S Rahmann - 22nd International Workshop on …, 2022 - drops.dagstuhl.de
Motivation. In biological sequence analysis, alignment-free (also known as k-mer-based)
methods are increasingly replacing mapping-and alignment-based methods for various …
methods are increasingly replacing mapping-and alignment-based methods for various …
'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 …
Efficient computation of spaced seed hashing with block indexing
Background Spaced-seeds, ie patterns in which some fixed positions are allowed to be wild-
cards, play a crucial role in several bioinformatics applications involving substrings counting …
cards, play a crucial role in several bioinformatics applications involving substrings counting …
S-conLSH: alignment-free gapped mapping of noisy long reads
Background The advancement of SMRT technology has unfolded new opportunities of
genome analysis with its longer read length and low GC bias. Alignment of the reads to their …
genome analysis with its longer read length and low GC bias. Alignment of the reads to their …