Fast alignment-free sequence comparison using spaced-word frequencies

kmacs: the k -mismatch average common substring approach to alignment-free sequence comparison

(2014) Chris-Andre Leimeister et al.   BIOINFORMATICS

Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches

(2014) Sebastian Horwege et al.   NUCLEIC ACIDS RESEARCH

kClust: fast and sensitive clustering of large protein sequence databases

(2013) Maria Hauser et al.   BMC BIOINFORMATICS

Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads

(2013) Kai Song et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis

(2012) Susana Vinga et al.   Algorithms for Molecular Biology

Alignment-free phylogeny of whole genomes using underlying subwords

(2012) Matteo Comin et al.   Algorithms for Molecular Biology

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts

(2012) Jonathan Göke et al.   BIOINFORMATICS

Alignment-free distance measure based on return time distribution for sequence analysis: Applications to clustering, molecular phylogeny and subtyping

(2012) Pandurang Kolekar et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Variable length local decoding and alignment-free sequence comparison

(2012) Gilles Didier et al.   THEORETICAL COMPUTER SCIENCE

A Phylogenetic Analysis of the Brassicales Clade Based on an Alignment-Free Sequence Comparison Method

(2012) Klas Hatje et al.   Frontiers in Plant Science

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Sequence embedding for fast construction of guide trees for multiple sequence alignment

(2010) Gordon Blackshields et al.   Algorithms for Molecular Biology

MS4 - Multi-Scale Selector of Sequence Signatures: an alignment-free method for the classification of biological sequences

(2010) Eduardo Corel et al.   BMC BIOINFORMATICS

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics

(2009) Fabian Schreiber et al.   BMC BIOINFORMATICS

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

Estimating Mutation Distances from Unaligned Genomes

(2009) Bernhard Haubold et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions

(2009) Gregory E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic DNA k-mer spectra: models and modalities

(2009) Benny Chor et al.   GENOME BIOLOGY