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On the Linear-Cost Subtree-Transfer Distance between Phylogenetic Trees

1999
*
Algorithmica
*

Computing

doi:10.1007/pl00008273
fatcat:a55jxp6dofbw3eh56vdrqpcoue
*the**linear*-*cost**subtree*-*transfer**distance**between*two w eighted*phylogenetic**trees*is NP-hard, provided we a l l o w m ultiple leaves of a*tree*to share*the*same label (i.e.*the**trees*are not ...*The**linear*-*cost**subtree*-*transfer**distance*is in fact identical to*the*nni*distance**on*unweighted phylogenies. 2. ... Hein for explaining to us*the*biological motivations for comparing weighted phylogenies and studying*the**linear*-*cost**subtree*-*transfer**distance*, respectively, T akashi Yokomori, Shengke Y u, and Louxin ...##
###
Page 6727 of Mathematical Reviews Vol. , Issue 2000i
[page]

2000
*
Mathematical Reviews
*

[Tromp, John] (NL-MATH; Amsterdam)

*On**the**linear*-*cost**subtree*-*transfer**distance**between**phylogenetic**trees*. (English summary) Algorithmica 25 (1999), no. 2-3, 176-195. ...*The**linear*-*cost**subtree*-*transfer**distance*is in fact identical to*the*nni*distance**on*unweighted phylogenies. 2. ...##
###
Nearest Neighbor Interchange and Related Distances
[chapter]

2014
*
Encyclopedia of Algorithms
*

However, both unicast/multicast routing game and multicast

doi:10.1007/978-3-642-27848-8_256-2
fatcat:hz7j6d44praz5ef4w62q6dcrya
*cost*sharing game are*one*folded:*the*unicast/multicast routing game does not take*the*receivers into account while*the*multicast*cost*sharing ...*The*first and foremost,*the*upper bound and lower bound*on*˛still have a gap of r if*the*multicast system is˛-stable; and a gap of 2r if*the*multicast system is˛-Nash stable. ... 2-approximation algorithm for*the**linear*-*cost**subtree*-*transfer**distance**on*weighted evolutionary*trees*. ...##
###
Nearest Neighbor Interchange and Related Distances
[chapter]

2016
*
Encyclopedia of Algorithms
*

However, both unicast/multicast routing game and multicast

doi:10.1007/978-1-4939-2864-4_256
fatcat:baryoj74szfutnczeqpjq2ttw4
*cost*sharing game are*one*folded:*the*unicast/multicast routing game does not take*the*receivers into account while*the*multicast*cost*sharing ...*The*first and foremost,*the*upper bound and lower bound*on*˛still have a gap of r if*the*multicast system is˛-stable; and a gap of 2r if*the*multicast system is˛-Nash stable. ... 2-approximation algorithm for*the**linear*-*cost**subtree*-*transfer**distance**on*weighted evolutionary*trees*. ...##
###
Nearest Neighbor Interchange and Related Distances
[chapter]

2008
*
Encyclopedia of Algorithms
*

However, both unicast/multicast routing game and multicast

doi:10.1007/978-0-387-30162-4_256
fatcat:45i6bhsce5dx3mfkzmdwt6m2oi
*cost*sharing game are*one*folded:*the*unicast/multicast routing game does not take*the*receivers into account while*the*multicast*cost*sharing ...*The*first and foremost,*the*upper bound and lower bound*on*˛still have a gap of r if*the*multicast system is˛-stable; and a gap of 2r if*the*multicast system is˛-Nash stable. ... 2-approximation algorithm for*the**linear*-*cost**subtree*-*transfer**distance**on*weighted evolutionary*trees*. ...##
###
High Performance Phylogenetic Analysis With Maximum Parsimony on Reconfigurable Hardware

2011
*
IEEE Transactions on Very Large Scale Integration (vlsi) Systems
*

*The*hardware architecture consists in a

*linear*systolic array composed of 20 processing elements each of which performing Sankoff's algorithm for a different

*tree*topology in parallel. ... We present in this paper

*the*detailed field-programmable gate-array (FPGA) design of

*the*Maximum Parsimony method for molecular-based

*phylogenetic*analysis and its implementation

*on*

*the*nodes of an FPGA ... There are various

*cost*schemes which can be represented as a

*cost*matrix that assigns a

*cost*for

*the*change

*between*each pair of character states. ...

##
###
A high performance FPGA-based core for phylogenetic analysis with Maximum Parsimony method

2009
*
2009 International Conference on Field-Programmable Technology
*

We present in this paper

doi:10.1109/fpt.2009.5377652
fatcat:mpec4zmpejbmvlmetletnzzeam
*the*detailed FPGA design of*the*Maximum Parsimony method for molecular-based*phylogenetic*analysis and its implementation*on*a Xilinx Virtex-4 FPGA chip. ...*The*hardware architecture consists of a*linear*systolic array composed of 20 processing elements each of which performing*the*Sankoff's algorithm for a different*tree*topology in parallel. ... There are various*cost*schemes which can be represented as a*cost*matrix that assigns a*cost*for*the*change*between*each pair of character states. ...##
###
A reconstruction problem for a class of phylogenetic networks with lateral gene transfers

2015
*
Algorithms for Molecular Biology
*

, and a set of extra secondary arcs

doi:10.1186/s13015-015-0059-z
pmid:26691555
pmcid:PMC4683721
fatcat:753gdv5lfzgvlnd4prmo5oztku
*between*nodes in this*tree*representing lateral gene*transfers*. ... We then give an algorithm that, given a set of pairwise different*phylogenetic**trees*T 0 , T 1 , . . . , T k*on**the*same set of taxa, outputs, when it exists,*the*LGT network that satisfies these conditions ... Acknowledgements We thank*the*anonymous reviewers for many comments and suggestions that have substantially improved*the*quality and readability of*the*paper. ...##
###
Scatter search with path relinking for phylogenetic inference

2006
*
European Journal of Operational Research
*

method based

doi:10.1016/j.ejor.2004.08.013
fatcat:jn4jyhobsjhvrfb3mcqjtr5kfq
*on*internal rotations of*subtrees*. ... We propose*the*use of scatter search with path relinking for*the*inference of*phylogenetic**trees*. Solutions are here represented as*trees*whose leaves span*the*set of species under study. ... Thanks are due to*the*anonymous reviewers for their detailed comments, and to Dr. Moscato for continuous (and compelling) discussions*on*bioinformatics. ...##
###
Rapidly Computing the Phylogenetic Transfer Index
[article]

2019
*
biorxiv/medrxiv
*
pre-print

Given

doi:10.1101/743948
fatcat:nagponaznfbxpf6p2m7h4soikq
*trees*T and T_o*on**the*same taxon set,*the**transfer*index φ(b, T_o ) is*the*number of taxa that need to be ignored so that*the*bipartition induced by branch b in T is equal to some bipartition in ... Recently, Lemoine et al. [13] used*the**transfer*index to design a novel bootstrap analysis technique that improves*on*Felsenstein bootstrap*on*large, noisy data sets. ... First, we initialize*the*D values by computing*the*rooted*transfer**distance*from*the*empty*subtree*to every*subtree*in T o . ...##
###
Inference of a Phylogenetic Tree: Hierarchical Clustering versus Genetic Algorithm
[chapter]

2012
*
Lecture Notes in Computer Science
*

This paper compares

doi:10.1007/978-3-642-35101-3_26
fatcat:tbo5gdiz7jfyvjlqcmn5an36wy
*the*implementations and performance of two computational methods, hierarchical clustering and a genetic algorithm, for inference of*phylogenetic**trees*in*the*context of*the*artificial ... For a small problem space of*the*original species proposed by Camin (1965)*the*genetic algorithm was able to produce a solution which had a lower Fitch*cost*and was closer to*the*theoretical evolution ... Introduction*Phylogenetic**trees*are a diagrammatic representation of*the*evolutionary relationships*between*taxonomic units (TU). ...##
###
Codivergence of Mycoviruses with Their Hosts

2011
*
PLoS ONE
*

Additionally, we assessed

doi:10.1371/journal.pone.0022252
pmid:21829452
pmcid:PMC3146478
fatcat:zrxzoqrg5jgxvcjjmbkvkykrgy
*the*sensitivity of*the*co-*phylogenetic*tests to*the*settings for inferring virus*trees*from their genome sequences and approximate, taxonomy-based host*trees*. ... This is*the*first study of mycovirus-host codivergence, and*the*results shed light not only*on*how mycovirus biology affects their co-*phylogenetic*relationships, but also*on*their presumable host range ... Hence,*one*might interpret*the*congruence*between*mycovirus and host phylogenies as indicative of a little probability of lateral*transfer**between*hosts, based*on**the*assumption that otherwise resource ...##
###
Efficient Parallel Computation of Nearest Neighbor Interchange Distances
[article]

2012
*
arXiv
*
pre-print

*The*nni-

*distance*is a well-known

*distance*measure for

*phylogenetic*

*trees*. ... Given two

*phylogenetic*

*trees*T1 and T2

*on*

*the*same set of taxa and with

*the*same multi-set of edge-weights,

*the*algorithm constructs a sequence of nni-operations of weight at most O(log n) \cdot opt, where ... Furthermore, they observed that

*the*nni-

*distance*is identical to

*the*

*linear*-

*cost*

*subtree*-

*transfer*

*distance*

*on*unweighted phylogenies [DHJ + 99] and gave an outline of an exact algorithm for

*distance*-restricted ...

##
###
Scalable Phylogenetics through Input Preprocessing
[chapter]

2010
*
Advances in Intelligent and Soft Computing
*

*Phylogenetic*reconstruction is

*one*of

*the*fundamental problems in computational biology. ...

*The*combinatorial explosion of

*the*state space and

*the*complexity of mathematical models impose practical limits

*on*workable problem sizes. ... Roberto Blanco was supported by Grant AP2008-03447 from

*the*Spanish Ministry of Education. ...

##
###
MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers
[article]

2017
*
bioRxiv
*
pre-print

When a set of

doi:10.1101/127548
fatcat:f4lwbd4arrh3ljgl2hf5oyyuze
*transfers*is detected by interpreting*the**phylogenetic*discordance*between*gene*trees*and a species*tree*,*the*set of all deduced time constraints can be used to rank*the*species*tree*, {\em ... In most conditions*the*obtained ranked*tree*is very close to*the*real*one*, confirming*the*potential of dating*the*history of life with*transfers*by maximizing time consistency. ... 1 , S r 2 ) is*the*Kendall*distance**between**the*two ranked*trees*. ...
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