Alignment-free phylogenetics and population genetics

AGP: A Multimethods Web Server for Alignment-Free Genome Phylogeny

(2013) J. Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Co-phylog: an assembly-free phylogenomic approach for closely related organisms

(2013) Huiguang Yi et al.   NUCLEIC ACIDS RESEARCH

A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences

(2011) David J Russell et al.   BMC BIOINFORMATICS

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

(2011) G. E. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alignment-free estimation of nucleotide diversity

(2010) Bernhard Haubold et al.   BIOINFORMATICS

Genetic hitchhiking versus background selection: the controversy and its implications

(2010) W. Stephan   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Efficient estimation of pairwise distances between genomes

(2009) Mirjana Domazet-Lošo et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A fungal phylogeny based on 82 complete genomes using the composition vector method

(2009) Hao Wang et al.   BMC EVOLUTIONARY BIOLOGY

Estimating Mutation Distances from Unaligned Genomes

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

Alignment-Free Sequence Comparison (I): Statistics and Power

(2009) Gesine Reinert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution

(2009) S.-R. Jun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Comparison of alignment free string distances for complete genome phylogeny

(2009) Frédéric Guyon et al.   Advances in Data Analysis and Classification

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction

(2008) K. Yang et al.   NUCLEIC ACIDS RESEARCH