Measuring the distance between multiple sequence alignments. Blackburne, B. P. & Whelan, S. Bioinformatics, 28(4):495–502, February, 2012.
Measuring the distance between multiple sequence alignments [link]Paper  doi  bibtex   
@article{blackburne_measuring_2012,
	title = {Measuring the distance between multiple sequence alignments},
	volume = {28},
	issn = {1367-4803, 1460-2059},
	url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btr701},
	doi = {10.1093/bioinformatics/btr701},
	language = {en},
	number = {4},
	urldate = {2016-08-31},
	journal = {Bioinformatics},
	author = {Blackburne, B. P. and Whelan, S.},
	month = feb,
	year = {2012},
	pages = {495--502},
}

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