Alignment-Free Genome Tree Inference by Learning Group-Specific Distance Metrics

A sub-cubic time algorithm for computing the quartet distance between two general trees

(2011) Jesper Nielsen et al.   Algorithms for Molecular Biology

Taxonomic metagenome sequence assignment with structured output models

(2011) Kaustubh R Patil et al.   NATURE METHODS

Predicting Plasmid Promiscuity Based on Genomic Signature

(2010) H. Suzuki et al.   JOURNAL OF BACTERIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Estimation of bacterial species phylogeny through oligonucleotide frequency distances

(2009) Mahoko Takahashi et al.   GENOMICS

Composition vector approach to whole-genome-based prokaryotic phylogeny: Success and foundations

(2009) Qiang Li et al.   JOURNAL OF BIOTECHNOLOGY

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

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

Phylogenetic Signals in DNA Composition: Limitations and Prospects

(2009) J. Mrazek   MOLECULAR BIOLOGY AND EVOLUTION

CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes

(2009) Z. Xu et al.   NUCLEIC ACIDS RESEARCH

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

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

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

Database resources of the National Center for Biotechnology Information

(2008) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

Habitat-Lite: A GSC Case Study Based on Free Text Terms for Environmental Metadata

(2008) Lynette Hirschman et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY