RAMBAUT, A., AND N. GRASSLY. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235--238. Home/Search Document Not in Database Summary Related Articles Check |
This paper is cited in the following contexts:
A Collapsing Method for the Efficient Recovery of Optimal.. - Hu, Kearney, Badger (Correct)
....tree topologies with varying branch length composition, on input leaves sizes: 30, 50, 75. We than generated sequence datasets by evolving sequences along these topologies using the HYK model of evolution with perturbations to its various parameters. The sequences were generated using Seq Gen [11]. For the tree topologies we chose: from the tree of the set of 218 representative prokaryotic sequences from the RDP database: denoted SSU 30, SSU 30b. from the RDP prokaryotic representative tree from the RDP database, denoted SSU 50; SSU 50b, as well as the 51 taxon Eutherian tree, denoted ....
Rambaut, A., and Grassly, N. Seq-gen: An application for the monte carlo simulation of dna sequence evolution along phylogenetic trees. Comp. Appl. Biosci. 13 (1997), 235-238.
Reconstructing Optimal Phylogenetic Trees: A Challenge in.. - Moret, Warnow (Correct)
....at the base of the edge is the product of the edge length by the sequence length. In the following we write # e to denote the average edge length in a collection of trees which is just 500 times the scaling factor. We generated random DNA sequences for the root and used the program Seq Gen [28] to evolve these sequences down the tree under the Jukes Cantor model of evolution, thus producing sets of sequences at the leaves, our synthetic datasets. Because the number of distinct unrooted, leaf labelled trees on n leaves is (2n 5) and because our input space is further expanded by the ....
A. Rambaut and N. C. Grassly. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comp. Applic. Biosci., 13:235--238, 1997.
A Collapsing Method for the Efficient Recovery of Optimal.. - Hu, Badger, Kearney (2003) (Correct)
....tree topologies with varying branch length composition, on input leaves sizes: 30, 50, 75. We than generated sequence datasets by evolving sequences along these topologies using the HYK model of evolution with perturbations to its various parameters. The sequences were generated using Seq Gen [11]. For the tree topologies we chose: from the tree of the set of 218 representative prokaryotic sequences from the RDP database: denoted SSU 30, SSU 30b. from the RDP prokaryotic representative tree from the RDP database, denoted SSU 50; SSU 50b, as well as the 51 taxon Eutherian tree, denoted ....
Rambaut, A., and Grassly, N. Seq-gen: An application for the monte carlo simulation of dna sequence evolution along phylogenetic trees. Comp. Appl. Biosci. 13 (1997), 235-238.
Performance Study of Phylogenetic Methods: - Unweighted Quartet Methods (Correct)
....of the edge. We then scaled each such base model tree by a multiplicative factor, ranging from 10 7 to 10 3 . This process produces Jukes Cantor trees with # e values ranging from a minimum of 10 7 to a maximum of 1. We generated random DNA sequences for the root and used the program Seq Gen [23] to evolve these sequences down the tree under the Jukes Cantor model of evolution, thus producing sets of sequences at the leaves, our synthetic datasets. 4.3. Statistical Considerations Because the number of distinct unrooted, leaf labelled trees on n leaves is (2n 5) and because our ....
Rambaut, A., and Grassly, N.C., "Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees," Comp. Applic. Biosci. 13 (1997), 235--238.
A Collapsing Method for Efficient Recovery of Optimal Edges in.. - Hu (2002) (Correct)
....space might be interesting. Currently a more substantial simulation study is in progress, where ten random topologies on taxon set of size: 30, 50, 70, and 100 are randomly sampled from the RDP database. For each topology, we adopt the HYK model [33] of evolution of sequences using the SeqGen [40] sequence generator along the tree topologies using a wide spectrum of parameter values on the HYK model of evolution as follows: The default transversion translation rate of: 4 : 1 . A rate heterogeneity of: # = 0.5, 1.0, 2.0 . Leaves of sequence lengths: 500, 1000, 2000 . ....
Rambaut, A., and Grassly, N. Seq-gen: An application for the monte carlo simulation of dna sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13 (1997).
An Investigation of Phylogenetic Likelihood Methods - Williams, Moret (2003) (1 citation) (Correct)
....our experiments, the deviation factor, c, was set to 4. Hence, the expected value each branch length is multiplied by is 1.36. 3.2 DNA Sequence Evolution Once model trees are constructed, sequences are generated based on a model of evolution. The software used for sequence evolution is Seq Gen [17]. We generated sequences under the Kimura 2 parameter (K2P) 8] Gamma [25] model of DNA sequence evolution, one of the standard models for studying the performance of phylogenetic reconstruction methods. Under K2P, each site evolves down the tree under the Markov assumption. In this model, ....
A. Rambaut and N. C. Grassly. Seq-gen: An application for the monte carlo simulation of dna sequence evolution along phylogenetic trees. Comp. Appl. Biosci., 13:235--238, 1997.
The Performance of Phylogenetic Methods on Trees of.. - Nakhleh, Roshan.. (2001) (Correct)
....130 different processors running the Debian Linux operating system. We also had nighttime use of approximately 150 Pentium III processors located in public undergraduate laboratories. Software: We used Sanderson s r8s package for generating birth death trees [17] and the program Seq Gen [15] to randomly generate a DNA sequence for the root and evolve it through the tree under K2P Gamma model of evolution. We calculated evolutionary distances appropriately for the model (see [11] In the presence of saturation (that is, datasets in which some distances could not be calculated because ....
A. Rambaut and N. C. Grassly. Seq-gen: An application for the Monte Carlo simulation of dna sequence evolution along phylogenetic trees. Comp. Appl. Biosci., 13:235--238, 1997.
Designing Fast Converging Phylogenetic Methods - Nakhleh, Roshan, John, Sun.. (2001) (Correct)
....boxes acting as file and checkpoint servers) The SCOUT cluster is funded by NSF EIA 9985991 and shared among five researchers. In addition, we also had nighttime use of approximately 150 Pentium III processors located in public undergraduate laboratories. Software: We used the program Seq Gen [26] to randomly generate a DNA sequence for the root and evolve it through the tree under the JC model of evolution and the K2P Gamma model. We calculate evolutionary distances appropriately for each model (see [22] The software for DCM NJ was written by Daniel Huson. To calculate the maximum ....
Rambaut, A., and Grassly, N. C., "Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees," Comp. Applic. Biosci. 13 (1997), 235--238.
An Approximation Algorithm for Character Compatibility and Fast.. - Tsang (2000) (Correct)
....the model of evolution is stochastic, we will run the above procedure multiple times to obtain reliable results. Several packages were used to help implement the simulation. We used the DNADIST program in the PHYLIP [30] package to compute distance matrices from sequence data. The SEQ GEN program [57] was used to generate sequences along a tree based on the K2P model. Finally, the LISTTREE program from [74] was used to generate random tree topologies. Trees With Long Edges To rst test whether the OSM is at all functional, we ran the simulation on a randomly generated tree with relatively ....
Rambaut, A. and Grassly, N.C. 1996. Seq-Gen: an application for the monte carlo simulation of dna sequence evolution along phylogenetic trees
Performance Study of Phylogenetic Methods: (Unweighted) .. - John, Warnow, Moret.. (Correct)
....We then scaled each such base model tree by a multiplicative factor, ranging from 10 7 to 10 3 . This process produces Jukes Cantor trees with e values ranging from a minimum of 10 7 to a maximum of 1. We generated random DNA sequences for the root and used the program Seq Gen 4 [20] to evolve these sequences down the tree under the Jukes Cantor model of evolution, thus producing sets of sequences at the leaves, our synthetic datasets. 4.3 Statistical considerations. Because the number of distinct unrooted, leaf labelled trees on n leaves is (2n 5) and because our input ....
Rambaut, A., and Grassly, N.C., \Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees," Comp. Applic. Biosci. 13 (1997), 235-238.
Bayesian Phylogenetic Inference via Markov Chain Monte Carlo .. - Mau, Newton, Larget (1998) (6 citations) (Correct)
....a simulation study. We generated ten synthetic data sets analogous to the cichlid data set. Each one had 32 aligned sequences of length 1044, separated into blocks of sites corresponding to the three codon positions, and each one was obtained using the simulation software Seq Gen version 1. 04 from Rambaut and Grassly (1996). To mimic the complexity of the cichlid problem, we fixed the true phylogeny in this simulation equal to one sampled from the posterior in Section 7. In particular, the corresponding tree topology was the most probable one (Table 4) We also used the same substitution parameters as those obtained ....
Rambaut, A. and Grassly, N. C. (1996). Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. CABIOS 13, 235-238.
Recovering Branches on the Tree of Life: An Approximation .. - Kearney, Li, Tsang, Jiang (1999) (1 citation) (Correct)
....conducted as above where ordinal splits were ranked by redundancy. The simulation reveals that when the first 200 out of the 1225 ordinal splits are taken, over 90 of the nontrivial splits of the tree are recovered, on average. These simulations were implemented with the help of several packages [20, 8, 10, 23]. 4 Conclusions The main contribution of this paper is a PTAS for the FCC problem. That is, the PTAS approximates the optimal evolutionary tree to within a given accuracy in polynomial time. The effectiveness of the Ordinal Split Method and PTAS combination for inferring evolutionary trees ....
A. Rambaut and N. C Grassly. Seq--Gen: An application for the monte carlo simulation of dna sequence evolution along phylogenetic trees. Comput. Appl. Biosci., 1996. in press.
A Simple, Fast, and Accurate Algorithm to Estimate Large.. - Guindon (2003) (Correct)
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RAMBAUT, A., AND N. GRASSLY. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235--238.
Fast Neighbor Joining - Elias, Lagergren (2005) (Correct)
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A. Rambaut and N.C. Grassly. Seq-gen: An application for the monte carlo simulation of dna sequence evolution along phylogenetic trees. Comp.Appl.Biosci., 13:235--238, 1997.
Topological Rearrangements and Local Search Method for.. - Denis Bertrand And (Correct)
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A. Rambault and N. Grassly, "Seq-Gen: An Application for the Monte Carlo Simulation of DNA Sequence Evolution Along Phylogenetic Trees," Computer Applied Biosciences, vol. 13, pp. 235238, 1997.
Journal Of Computational Biology - Volume Number Mary (Correct)
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Rambaut, A., and Grassly, N.C. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13, 235--238.
Distance Corrections on Recombinant Sequences - Bryant, Huson, Kloepper.. (Correct)
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A. Rambaut and N.C. Grassly. Seq-gen: An application for the monte carlo simulation of DNA sequence evolution along phylogenetic trees. Comput.Appl.Biosci., 13:235--238, 1997.
A Collapsing Method for the Efficient Recovery of Optimal.. - Hu, Kearney, Badger (Correct)
No context found.
Rambaut, A., and Grassly, N. Seq-gen: An application for the monte carlo simulation of dna sequence evolution along phylogenetic trees. Comp. Appl. Biosci. 13 (1997), 235--238.
Fast and Accurate Phylogeny Reconstruction Algorithms Based.. - Desper, Gascuel (2002) (2 citations) (Correct)
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Rambaut, A., Grassly, N.C.: Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Computer Applications in the Biosciences 13 #1997# 235#238
A Collapsing Method for Efficient Recovery of Best Supported.. - Hu, Kearney (2002) (Correct)
No context found.
Rambaut, A., and Grassly, N. Seq-gen: An application for the monte carlo simulation of dna sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13 (1997).
Sequence-Length Requirements for Phylogenetic Methods - Moret, Roshan, Warnow (2002) (Correct)
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A. Rambaut and N. C. Grassly. Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comp. Appl. Biosci., 13:235--238, 1997.
Sequence-Length Requirements for Phylogenetic Methods - Moret, Roshan, Warnow (2002) (Correct)
No context found.
A. Rambaut and N. C. Grassly. Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comp. Appl. Biosci., 13:235--238, 1997.
The Accuracy of Fast Phylogenetic Methods for Large Datasets - Nakhleh, Moret, Roshan (2002) (1 citation) (Correct)
No context found.
A. Rambaut and N. C. Grassly. Seq-gen: An application for the Monte Carlo simulation of dna sequence evolution along phylogenetic trees. Comp. Appl. Biosci., 13:235--238, 1997.
TOPAL 2.0: Improved graphical method and statistical test for .. - McGuire, Wright (Correct)
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Rambaut,A. and Grassly,N. C. (1997) Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. CABIOS, 13, 235--238.
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