Evidence for a Relationship Between Algorithmic Scheme and Shape of Inferred Trees

Gascuel, Olivier

doi:10.1007/978-3-642-58250-9_13

Cited by 5 publications

(4 citation statements)

References 13 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Trees from processes known to produce different shapes are well separated in the metric that arises naturally from the scheme. This suggests applications in inferring evolutionary processes and to detecting tree shape bias ( Huelsenbeck and Kirkpatrick 1996 ; Gascuel 2000 ; Stam 2002 ). The structure and simplicity of this comparison tool carry a number of advantages.…”

Section: Discussionmentioning

confidence: 99%

“…Tree shapes carry information about the underlying evolutionary processes, and distributions of tree shapes under simple null models can be used to test hypotheses about evolution ( Mooers and Heard 1997 ; Blum and François 2006 ; Blum et al 2006 ; Purvis et al 2011 ; Wu and Choi 2015 ). Recent work also relates fitness, selection and a variety of ecological processes to tree shape ( Gascuel 2000 ; Hein et al 2004 ; Maia et al 2004 ; Wakeley and Wakeley 2009 ; Dayarian and Shraiman 2014 ; Manceau et al 2015 ). An additional motivation for studying the shapes of phylogenetic trees is that reconstructing branch lengths is challenging, particularly deep in a tree.…”

mentioning

confidence: 99%

See 1 more Smart Citation

A Metric on Phylogenetic Tree Shapes

Colijn

Plazzotta

2017

Systematic Biology

View full text Add to dashboard Cite

The shapes of evolutionary trees are influenced by the nature of the evolutionary process but comparisons of trees from different processes are hindered by the challenge of completely describing tree shape. We present a full characterization of the shapes of rooted branching trees in a form that lends itself to natural tree comparisons. We use this characterization to define a metric, in the sense of a true distance function, on tree shapes. The metric distinguishes trees from random models known to produce different tree shapes. It separates trees derived from tropical versus USA influenza A sequences, which reflect the differing epidemiology of tropical and seasonal flu. We describe several metrics based on the same core characterization, and illustrate how to extend the metric to incorporate trees’ branch lengths or other features such as overall imbalance. Our approach allows us to construct addition and multiplication on trees, and to create a convex metric on tree shapes which formally allows computation of average tree shapes.

show abstract

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

A Metric on Phylogenetic Tree Shapes

Colijn

Plazzotta

2017

Systematic Biology

View full text Add to dashboard Cite

show abstract

“…Trees from processes known to produce different shapes are well separated in the metric that arises naturally from the scheme. This suggests applications in inferring evolutionary processes and to detecting tree shape bias (Huelsenbeck & Kirkpatrick, 1996;Gascuel, 2000;Stam, 2002). The structure and simplicity of this comparison tool carry a number of advantages.…”

Section: Discussionmentioning

confidence: 99%

“…Tree shapes carry information about the underlying evolutionary processes, and distributions of tree shapes under simple null models can be used to test hypotheses about evolution (Mooers & Heard, 1997;Blum, François, & Janson, 2006;Purvis et al, 2011;Wu & Choi, 2015). Recent work also relates fitness, selection and a variety of ecological processes to tree shape (LP, Colato, & Fontanari, 2004;Dayarian & Shraiman, 2014;J Hein, 2004;Wakeley & Wakeley, 2009;Gascuel, 2000;Manceau et al, 2015). An additional motivation for studying the shapes of phylogenetic trees is that reconstructing branch lengths is challenging, particularly deep in a tree.…”

Section: Introductionmentioning

confidence: 99%

A metric on phylogenetic tree shapes

Colijn

Plazzotta

2016

Preprint

View full text Add to dashboard Cite

Abstract.-The shapes of evolutionary trees are influenced by the nature of the evolutionary process but comparisons of trees from different processes are hindered by the challenge of completely describing tree shape. We present a full characterization of the shapes of rooted branching trees in a form that lends itself to natural tree comparisons. We use this characterization to define a metric, in the sense of a true distance function, on tree shapes. The metric distinguishes trees from random models known to produce different tree shapes. It separates trees derived from tropical versus USA influenza A sequences, which reflect the differing epidemiology of tropical and seasonal flu. We describe several metrics based on the same core characterization, and illustrate how to extend the metric to incorporate trees' branch lengths or other features such as overall imbalance. Our approach allows us to construct addition and multiplication on trees, and to create a convex metric on tree shapes which formally allows computation of average tree shapes. [tree metric; phylodynamics; tree shapes]

show abstract

Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood

2005

View full text Add to dashboard Cite

Experiments with real datasets comprising 35-250 taxa show that, while indeed greatly reducing the amount of computation, our approach provides likelihood values at least as good as those of the best-known ML methods so far and is very robust to poor starting trees. Furthermore, combining our new SPR algorithm with local moves such as PHYML's nearest neighbor interchanges, the time needed to find good solutions can sometimes be reduced even more.

show abstract

Evidence for a Relationship Between Algorithmic Scheme and Shape of Inferred Trees

Cited by 5 publications

References 13 publications

A Metric on Phylogenetic Tree Shapes

A Metric on Phylogenetic Tree Shapes

A metric on phylogenetic tree shapes

Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood

Contact Info

Product

Resources

About