Strategies for Identifying the Optimal Length of K-mer in a Viral Phylogenomic Analysis using Genomic Alignment-free Method

Rosemary Braun, Systems Analysis of High-Throughput Data Advances in Experimental Medicine and Biology. ,vol. 844, pp. 153- 187 ,(2014) , 10.1007/978-1-4939-2095-2_8

Michael G. Sadovsky, Comparison of Real Frequencies of Strings vs. the Expected Ones Reveals the Information Capacity of Macromoleculae. Journal of Biological Physics. ,vol. 29, pp. 23- 38 ,(2003) , 10.1023/A:1022554613105

Liam J. Revell, phytools: an R package for phylogenetic comparative biology (and other things) Methods in Ecology and Evolution. ,vol. 3, pp. 217- 223 ,(2012) , 10.1111/J.2041-210X.2011.00169.X

Neha J. Varghese, Supratim Mukherjee, Natalia Ivanova, Konstantinos T. Konstantinidis, Kostas Mavrommatis, Nikos C. Kyrpides, Amrita Pati, Microbial species delineation using whole genome sequences Nucleic Acids Research. ,vol. 43, pp. 6761- 6771 ,(2015) , 10.1093/NAR/GKV657

David A. Morrison, Multiple sequence alignment for phylogenetic purposes Australian Systematic Botany. ,vol. 19, pp. 479- 539 ,(2006) , 10.1071/SB06020

S. Kullback, R. A. Leibler, On Information and Sufficiency Annals of Mathematical Statistics. ,vol. 22, pp. 79- 86 ,(1951) , 10.1214/AOMS/1177729694

O. Bonham-Carter, J. Steele, D. Bastola, Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis Briefings in Bioinformatics. ,vol. 15, pp. 890- 905 ,(2014) , 10.1093/BIB/BBT052

Yueyi Gao, Qiuwen Kou, Xinna Ge, Lei Zhou, Xin Guo, Hanchun Yang, Phylogenetic analysis of porcine epidemic diarrhea virus field strains prevailing recently in China Archives of Virology. ,vol. 158, pp. 711- 715 ,(2013) , 10.1007/S00705-012-1541-2

Weifeng Shi, Michael J. Carr, Linda Dunford, Chaodong Zhu, William W. Hall, Desmond G. Higgins, Identification of novel inter-genotypic recombinants of human hepatitis B viruses by large-scale phylogenetic analysis. Virology. ,vol. 427, pp. 51- 59 ,(2012) , 10.1016/J.VIROL.2012.01.030

Peter Simmonds, Methods for virus classification and the challenge of incorporating metagenomic sequence data. Journal of General Virology. ,vol. 96, pp. 1193- 1206 ,(2015) , 10.1099/JGV.0.000016