fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood

Olsen, Gary J.; Matsuda, Hideo; Hagstrom, Ray; Overbeek, Ross

doi:10.1093/bioinformatics/10.1.41

Cited by 814 publications

(704 citation statements)

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“…It is common for inference programs to start with a tree on three taxa and then build a tree by adding taxa sequentially. Software packages using sequential taxon addition, such as PHYLIP (Felsenstein 1995) and fastDNAml (Olsen et al 1994), do optimize the tree after addition using rearrangements; the question of strict sequential addition performance is still important in order to determine the amount of post-addition optimization required. Furthermore, "evolutionary placement algorithms" for large amounts of sequence data have been proposed whereby a "query" sequences are inserted into a fixed "reference tree" (Von Mering et al 2007;Berger and Stamatakis 2009).…”

Section: Discussionmentioning

confidence: 99%

Polyhedral Geometry of Phylogenetic Rogue Taxa

Cueto

Matsen

2010

Bull Math Biol

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It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this "rogue taxon" effect. In this paper we characterize the behavior of balanced minimum evolution (BME) phylogenetics on data sets of this type using tools from polyhedral geometry. First we show that for any distance matrix there exist distances to a "rogue taxon" such that the BME-optimal tree for the data set with the new taxon does not contain any nontrivial splits (bipartitions) of the optimal tree for the original data. Second, we prove a theorem which restricts the topology of BME-optimal trees for data sets of this type, thus showing that a rogue taxon cannot have an arbitrary effect on the optimal tree. Third, we computationally construct polyhedral cones that give complete answers for BME rogue taxon behavior when our original data fits a tree on four, five, and six taxa. We use these cones to derive sufficient conditions for rogue taxon behavior for four taxa, and to understand the frequency of the rogue taxon effect via simulation.

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Section: Discussionmentioning

confidence: 99%

Polyhedral Geometry of Phylogenetic Rogue Taxa

Cueto

Matsen

2010

Bull Math Biol

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“…Trees were also constructed from the data using maximum parsimony, maximum likelihood, and neighbor-joining, using the programs PAUP 3.1.1 (Swofford, 1993), fastDNAml (Olsen et al, 1994), and the PHYLIP programs DNADIST, SEQBOOT, and NEIGHBOR (Felsenstein, 1993). COMPONENT (Page, 1993a) was used to compare morphological and molecular trees for the lice using partition (d s ) and quartet (d q ) measures of tree similarity (Steel and Penny, 1993).…”

Section: Fig 4-continuedmentioning

confidence: 99%

A Different Tempo of Mitochondrial DNA Evolution in Birds and Their Parasitic Lice

Page

Lee

Becher

et al. 1998

Molecular Phylogenetics and Evolution

136

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“…The data set consists of sequence data for six loci: internal transcribed spacer of ribosomal DNA (ITS); NADH dehydrogenase, subunit F (ndhF); phytochrome B (phyB); ribulose 1,5-biphosphate carboxylase/oxygenase, large subunit (rbcL); RNA polymerase II, subunit (rpoC2); and granule bound starch synthase I (waxy). For each loci, a tree was built using the fastDNAmL program [21] by Heiko Schmidt [23]. As in [7], we looked at pairs of trees, reduced to their common taxa.…”

Section: Datamentioning

confidence: 99%

Efficiently Calculating Evolutionary Tree Measures Using SAT

Bonet

John

2009

Lecture Notes in Computer Science

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Abstract. We develop techniques to calculate important measures in evolutionary biology by encoding to CNF formulas and using powerful SAT solvers. Comparing evolutionary trees is a necessary step in tree reconstruction algorithms, locating recombination and lateral gene transfer, and in analyzing and visualizing sets of trees. We focus on two popular comparison measures for trees: the hybridization number and the rooted subtree-prune-and-regraft (rSPR) distance. Both have recently been shown to be NP-hard, and efficient algorithms are needed to compute and approximate these measures. We encode these as a Boolean formula such that two trees have hybridization number k (or rSPR distance k) if and only if the corresponding formula is satisfiable. We use state-of-the-art SAT solvers to determine if the formula encoding the measure has a satisfying assignment. Our encoding also provides a rich source of real-world SAT instances, and we include a comparison of several recent solvers (minisat, adaptg2wsat, novelty+p, Walksat, March KS and SATzilla).

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fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood

Cited by 814 publications

References 0 publications

Polyhedral Geometry of Phylogenetic Rogue Taxa

Polyhedral Geometry of Phylogenetic Rogue Taxa

A Different Tempo of Mitochondrial DNA Evolution in Birds and Their Parasitic Lice

Efficiently Calculating Evolutionary Tree Measures Using SAT

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