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k 阶简约系统发生网络空间的度量。

A Metric on the Space of kth-order reduced Phylogenetic Networks.

机构信息

School of Computer Science, Inner Mongolia University, Hohhot, 010021, P.R. China.

School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing, 100044, P.R. China.

出版信息

Sci Rep. 2017 Jun 9;7(1):3189. doi: 10.1038/s41598-017-03363-y.

DOI:10.1038/s41598-017-03363-y
PMID:28600511
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5466651/
Abstract

Phylogenetic networks can be used to describe the evolutionary history of species which experience a certain number of reticulate events, and represent conflicts in phylogenetic trees that may be due to inadequacies of the evolutionary model used in the construction of the trees. Measuring the dissimilarity between two phylogenetic networks is at the heart of our understanding of the evolutionary history of species. This paper proposes a new metric, i.e. kth-distance, for the space of kth-order reduced phylogenetic networks that can be calculated in polynomial time in the size of the compared networks.

摘要

系统发育网络可用于描述经历一定数量的网状事件的物种的进化历史，并表示可能由于构建树时使用的进化模型的不足而导致的系统发育树中的冲突。测量两个系统发育网络之间的相似度是我们理解物种进化历史的核心。本文提出了一种新的度量标准，即 k 阶简约系统发育网络的 k 阶距离，该度量标准可以在比较网络的大小的多项式时间内计算。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/161788995cce/41598_2017_3363_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/148e504d4c6b/41598_2017_3363_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/641218383175/41598_2017_3363_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/26351882268c/41598_2017_3363_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/897ef5abbd7b/41598_2017_3363_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/602514fe38fe/41598_2017_3363_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/bc7ac8c98053/41598_2017_3363_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/59f96daebab3/41598_2017_3363_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/8387693c0b3a/41598_2017_3363_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/161788995cce/41598_2017_3363_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/148e504d4c6b/41598_2017_3363_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/641218383175/41598_2017_3363_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/26351882268c/41598_2017_3363_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/897ef5abbd7b/41598_2017_3363_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/602514fe38fe/41598_2017_3363_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/bc7ac8c98053/41598_2017_3363_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/59f96daebab3/41598_2017_3363_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/8387693c0b3a/41598_2017_3363_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ee61/5466651/161788995cce/41598_2017_3363_Fig9_HTML.jpg

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本文引用的文献

1
A Metric on the Space of Partly Reduced Phylogenetic Networks.部分简约系统发育网络空间上的一种度量
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Genet Mol Res. 2014 Mar 6;13(1):1456-64. doi: 10.4238/2014.March.6.4.
5
BIMLR: a method for constructing rooted phylogenetic networks from rooted phylogenetic trees.BIMLR：一种从有根系统发生树构建有根系统发生网络的方法。
Gene. 2013 Sep 15;527(1):344-51. doi: 10.1016/j.gene.2013.06.036. Epub 2013 Jun 28.
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LNETWORK: an efficient and effective method for constructing phylogenetic networks.LNETWORK：一种构建系统发育网络的高效方法。
Bioinformatics. 2013 Sep 15;29(18):2269-76. doi: 10.1093/bioinformatics/btt378. Epub 2013 Jun 29.
7
Survey of MapReduce frame operation in bioinformatics.生物信息学中MapReduce框架操作的调查。
Brief Bioinform. 2014 Jul;15(4):637-47. doi: 10.1093/bib/bbs088. Epub 2013 Feb 7.
8
FastJoin, an improved neighbor-joining algorithm.FastJoin，一种改进的邻接法算法。
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9
Metrics on multilabeled trees: interrelationships and diameter bounds.多标记树的度量：相互关系和直径界限。
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A metric on the space of reduced phylogenetic networks.关于简化系统发育网络空间的测度。
IEEE/ACM Trans Comput Biol Bioinform. 2010 Apr-Jun;7(2):218-22. doi: 10.1109/TCBB.2009.2.