CAFE : aCcelerated Alignment-FrEe sequence analysis : Supplementary Material

Yang Young Lu,Kujin Tang,Jie Ren,Jed A. Fuhrman,Michael S. Waterman and Fengzhu Sun1,3∗ Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, CA, USA Department of Biological Sciences and Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, California, USA Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, China

[1]  Kai Song,et al.  Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics , 2015, Bioinform..

[2]  Sanjeev Galande,et al.  One size does not fit all: On how Markov model order dictates performance of genomic sequence analyses , 2012, Nucleic acids research.

[3]  Huiguang Yi,et al.  Co-phylog: an assembly-free phylogenomic approach for closely related organisms , 2010, Nucleic acids research.

[4]  D. Robinson,et al.  Comparison of phylogenetic trees , 1981 .

[5]  Se-Ran Jun,et al.  Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions , 2009, Proceedings of the National Academy of Sciences.

[6]  Gesine Reinert,et al.  Alignment-Free Sequence Comparison (I): Statistics and Power , 2009, J. Comput. Biol..

[7]  Daniel J. Blankenberg,et al.  28-way vertebrate alignment and conservation track in the UCSC Genome Browser. , 2007, Genome research.

[8]  B. Blaisdell A measure of the similarity of sets of sequences not requiring sequence alignment. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Se-Ran Jun,et al.  Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution , 2009, Proceedings of the National Academy of Sciences.

[10]  Korbinian Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..

[11]  Hong Luo,et al.  CVTree: a phylogenetic tree reconstruction tool based on whole genomes , 2004, Nucleic Acids Res..

[12]  Mark A. Ragan,et al.  Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer , 2016, Scientific Reports.

[13]  Gesine Reinert,et al.  Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics , 2010, J. Comput. Biol..

[14]  Minghua Deng,et al.  Comparison of metagenomic samples using sequence signatures , 2012, BMC Genomics.