Ancestral inference from gene trees by Griffiths, R

Ancestral inference on gene trees under selection. by Coop, G, Griffiths, R

“…The method is applied to a simulated data set and the gene tree presented in Verrelli et al. (2002).…”

The likelihood of gene trees under selective models by Coop, GM

“…This allows a unique perfect phylogeny, a gene tree, to be constructed from the configuration of mutations on the sample sequences. …”

Characterizing gene tree conflict in plastome-inferred phylogenies by Joseph F. Walker, Nathanael Walker-Hale, Oscar M. Vargas, Drew A. Larson, Gregory W. Stull

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Inference from gene trees in a subdivided population. by Bahlo, M, Griffiths, R

“…This paper studies gene trees in subdivided populations which are constructed as perfect phylogenies from the pattern of mutations in a sample of DNA sequences and presents a new recursion for the probability distribution of such gene trees. …”

The worldwide holoparasitic Apodanthaceae confidently placed in the Cucurbitales by nuclear and mitochondrial gene trees by Renner Susanne S, Filipowicz Natalia

“…Analyses were performed at the nucleotide and at the amino acid level. Both gene trees agree with angiosperm phylogenies found in other studies using more genes. …”
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Phylogenetic Discordance between Species Tree and Functional Gene Trees of Fagaceous Genera by Min-Xin Luo, Chien-Ti Chao, Jui-Tse Chang, Pei-Chun Liao

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A Linear-Time Algorithm for the Isometric Reconciliation of Unrooted Trees by Broňa Brejová, Rastislav Královič

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Species-level para- and polyphyly in DNA barcode gene trees: Strong operational bias in European Lepidoptera by Mutanen, M, Kivelä, S, Vos, R, Doorenweerd, C, Ratnasingham, S, Hausmann, A, Huemer, P, Dincă, V, van Nieukerken, E, Lopez-Vaamonde, C, Vila, R, Aarvik, L, Decaëns, T, Efetov, K, Hebert, P, Johnsen, A, Karsholt, O, Pentinsaari, M, Rougerie, R, Segerer, A, Tarmann, G, Zahiri, R, Godfray, H

“…This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, nonmonophyly has been reported as being common in mitochondrial DNA gene trees. …”

A new gene tree algorithm employing DNA sequences of bovine genome using discrete Fourier transformation. by Roxana Abadeh, Mehdi Aminafshar, Mostafa Ghaderi-Zefrehei, Mohammad Chamani

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Monophyly and transoceanic dispersal in the widespread floating club-rush clade, Isolepis subgenus Fluitantes (Cyperaceae) by Jan-Adriaan Viljoen, Terry Hedderson, Charlotte Sletten Bjorå, Muthama Muasya

Subjects: “…Gene tree incongruence…”
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Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on <i>Paphiopedilum</i> Pfitz. (Orchidaceae) by Marcin Górniak, Dariusz L. Szlachetko, Natalia Olędrzyńska, Aleksandra M. Naczk, Agata Mieszkowska, Lidia Boss, Marek S. Ziętara

“…We assumed that an incongruence in nuclear gene trees is caused by ancestral homoploid hybridization. …”
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Taxonomic classification on phylogenic information appears a debatable approach: Lessons from the order Cypriniformes by Himanshu Priyadarshi, Rekha Das, Gowrimanohari Rakkannan

Subjects: “…gene tree…”
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Predicting the Evolution of Syntenies—An Algorithmic Review by Nadia El-Mabrouk

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Future trypanosomatid phylogenies: refined homologies, supertrees and networks by Stothard JR

Subjects: “…gene trees…”
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On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer by Mathieu Gascon, Nadia El-Mabrouk

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How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships? by Zeyuan Chen, Michael Schrödl

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Relative timing information and orthology in evolutionary scenarios by David Schaller, Tom Hartmann, Manuel Lafond, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth

Subjects: “…Gene tree…”
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The dynamics of introgression across an avian radiation by Sonal Singhal, Graham E. Derryberry, Gustavo A. Bravo, Elizabeth P. Derryberry, Robb T. Brumfield, Michael G. Harvey

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Phylogenomic Coalescent Analyses of Avian Retroelements Infer Zero-Length Branches at the Base of Neoaves, Emergent Support for Controversial Clades, and Ancient Introgressive Hybr... by John Gatesy, Mark S. Springer

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