# Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees

@article{Kalaghatgi2016FamilyJoiningAF, title={Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees}, author={Prabhav Kalaghatgi and Nico Pfeifer and Thomas Lengauer}, journal={Molecular Biology and Evolution}, year={2016}, volume={33}, pages={2720 - 2734} }

The widely used model for evolutionary relationships is a bifurcating tree with all taxa/observations placed at the leaves. This is not appropriate if the taxa have been densely sampled across evolutionary time and may be in a direct ancestral relationship, or if there is not enough information to fully resolve all the branching points in the evolutionary tree. In this article, we present a fast distance-based agglomeration method called family-joining (FJ) for constructing so-called generally…

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## References

SHOWING 1-10 OF 29 REFERENCES

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

- BiologyMolecular biology and evolution
- 1987

The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.

Building trees, hunting for trees, and comparing trees : theory and methods in phylogenetic analysis

- Computer Science
- 1997

It is proved that there exist rules of every order that cannot be reduced to lower order rules, and several new NPcompleteness results and a list of standard NP-complete phylogenetic problems are discussed.

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

- Computer Science, BiologyBioinform.
- 2005

This paper presents the latest release of the program RAxML-III for rapid maximum likelihood-based inference of large evolutionary trees which allows for computation of 1.000-taxon trees in less than 24 hours on a single PC processor.

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.

- Computer ScienceMolecular biology and evolution
- 1997

An improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei, BIONJ, follows the same agglomerative scheme as NJ, which consists of iteratively picking a pair of taxa, creating a new mode which represents the cluster of these taxa and reducing the distance matrix by replacing both taxa by this node.

Rapid Evaluation of Least-Squares and Minimum-Evolution Criteria on Phylogenetic Trees

- Computer Science
- 1998

We present fast new algorithms for evaluating trees with respect to least squares and minimum evolution (ME), the most commonly used criteria for inferring phylogenetic trees from distance data.…

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration

- BiologyPLoS Comput. Biol.
- 2014

A Bayesian Markov Chain Monte Carlo algorithm is developed and implemented to infer sampled ancestor trees, that is, trees in which sampled individuals can be direct ancestors of other sampled individuals, and applies its phylogenetic inference accounting for sampled ancestors to epidemiological data.

A note on the neighbor-joining algorithm of Saitou and Nei.

- Computer ScienceMolecular biology and evolution
- 1988

The proof given by Saitou and Nei that the correct tree is recovered if D is treelike is incorrect is supplied, and an alternative formulation that runs in time 0( N3), where N is the number of operational taxonomic units (OTUs) .

Factors affecting the errors in the estimation of evolutionary distances between sequences.

- BiologyMolecular biology and evolution
- 2003

The accuracy of likelihood-based distance estimates is much higher than those based on log transform formulae, particularly in cases where there is a large range of timescales involved in the rate matrix and when the ratio of transition to transversion rates is large.

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

- BiologyMolecular biology and evolution
- 2012

The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7 is presented, which implements a family of Markov chain Monte Carlo algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses.

Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology

- Biology
- 1971

A method is presented that is asserted to provide all hypothetical ancestral character states that are consistent with describing the descent of the present-day character states in a minimum number of changes of state using a predetermined phylogenetic relationship among the taxa represented.