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DATE 2017-04-01

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MESSAGE
DATE 2017-04-05
FROM ruben
SUBJECT Subject: [Learn] Bounds for phylogenetic network space metrics
From learn-bounces-at-nylxs.com Wed Apr 5 07:58:20 2017
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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.




















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:
href="https://arxiv.org/abs/1702.05609">arXiv:1702.05609
[q-bio.PE]
  (or href="https://arxiv.org/abs/1702.05609v2">arXiv:1702.05609v2
[q-bio.PE]
for this version)






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