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DATE | 2017-04-05 |
FROM | ruben
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SUBJECT | Subject: [Learn] Bounds for phylogenetic network space metrics
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From learn-bounces-at-nylxs.com Wed Apr 5 07:58:20 2017 Return-Path: X-Original-To: archive-at-mrbrklyn.com Delivered-To: archive-at-mrbrklyn.com Received: from www.mrbrklyn.com (www.mrbrklyn.com [96.57.23.82]) by mrbrklyn.com (Postfix) with ESMTP id 06B56163F8E; Wed, 5 Apr 2017 07:58:20 -0400 (EDT) X-Original-To: learn-at-nylxs.com Delivered-To: learn-at-nylxs.com Received: from [10.0.0.56] (stat50.mrbrklyn.com [10.0.0.56]) by mrbrklyn.com (Postfix) with ESMTP id 33413163F77 for ; Wed, 5 Apr 2017 07:58:17 -0400 (EDT) To: learn-at-nylxs.com From: ruben Message-ID: <58E4DBD9.5040206-at-mrbrklyn.com> Date: Wed, 5 Apr 2017 07:58:17 -0400 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:38.0) Gecko/20100101 Icedove/38.8.0 MIME-Version: 1.0 Subject: [Learn] Bounds for phylogenetic network space metrics X-BeenThere: learn-at-nylxs.com X-Mailman-Version: 2.1.17 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Content-Type: multipart/mixed; boundary="===============0275565865==" Errors-To: learn-bounces-at-nylxs.com Sender: "Learn"
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https://arxiv.org/abs/1702.05609
Andrew Francis , Katharina Huber , Vincent Moulton , Taoyang Wu
(Submitted on 18 Feb 2017 (v1 ), last revised 8 Mar 2017 (this version, v2))
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which every vertex has degree 1 or 3 and whose leaf-set is a fixed set $X$ of taxa. This space, denoted $\mathcal{N}(X)$, is defined in terms of two operations on networks -- the nearest neighbor interchange and triangle operations -- which can be used to transform any network with leaf set $X$ into any other network with that leaf set. In particular, it gives rise to a metric $d$ on $\mathcal N(X)$ which is given by the smallest number of operations required to transform one network in $\mathcal N(X)$ into another in $\mathcal N(X)$. The metric generalizes the well-known NNI-metric on phylogenetic trees which has been intensively studied in the literature. In this paper, we derive a bound for the metric $d$ as well as a related metric $d_{N\!N\!I}$ which arises when restricting $d$ to the subset of $\mathcal{N}(X)$ consisting of all networks with $2(|X|-1+i)$ vertices, $i \ge 1$. We also introduce two new metrics on networks -- the SPR and TBR metrics -- which generalize the metrics on phylogenetic trees with the same name and give bounds for these new metrics. We expect our results to eventually have applications to the development and understanding of network search algorithms.
Comments: 17 pages, 5 figures. This version has a new figure to illustrate Lemma 3.2, and a new Corollary 5.7 that bounds the distance between networks in different tiers Subjects: Populations and Evolution (q-bio.PE); Combinatorics (math.CO) Cite as: arXiv:1702.05609 [q-bio.PE] (or arXiv:1702.05609v2 [q-bio.PE] for this version)
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https://arxiv.org/abs/1702.05609
Andrew Francis, href="https://arxiv.org/find/q-bio/1/au:+Huber_K/0/1/0/all/0/1">Katharina Huber, href="https://arxiv.org/find/q-bio/1/au:+Moulton_V/0/1/0/all/0/1">Vincent Moulton, href="https://arxiv.org/find/q-bio/1/au:+Wu_T/0/1/0/all/0/1">Taoyang Wu Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which every vertex has degree 1 or 3 and whose leaf-set is a fixed set $X$ of taxa. This space, denoted $\mathcal{N}(X)$, is defined in terms of two operations on networks -- the nearest neighbor interchange and triangle operations -- which can be used to transform any network with leaf set $X$ into any other network with that leaf set. In particular, it gives rise to a metric $d$ on $\mathcal N(X)$ which is given by the smallest number of operations required to transform one network in $\mathcal N(X)$ into another in $\mathcal N(X)$. The metric generalizes the well-known NNI-metric on phylogenetic trees which has been intensively studied in the literature. In this paper, we derive a bound for the metric $d$ as well as a related metric $d_{N\!N\!I}$ which arises when restricting $d$ to the subset of $\mathcal{N}(X)$ consisting of all networks with $2(|X|-1+i)$ vertices, $i \ge 1$. We also introduce two new metrics on networks -- the SPR and TBR metrics -- which generalize the metrics on phylogenetic trees with the same name and give bounds for these new metrics. We expect our results to eventually have applications to the development and understanding of network search algorithms.
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