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2,417
Impacts of Terraces on Phylogenetic Inference
, 2015
"... Abstract.—Terraces are sets of trees with precisely the same likelihood or parsimony score, which can be induced by missing sequences in partitioned multi-locus phylogenetic data matrices. The potentially large set of trees on a terrace can be characterized by enumeration algorithms or consensus met ..."
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methods that exploit the pattern of partial taxon coverage in the data, independent of the sequence data themselves. Terraces can add ambiguity and complexity to phylogenetic inference, particularly in settingswhere inference is already challenging: data sets withmany taxa and relatively few loci
Orthologous Repeats and Phylogenetic Inference
"... Determining phylogenetic relationships between species is a difficult problem, and many phylogenetic relationships remain unresolved, even among eutherian mammals. Repetitive elements provide excellent markers for phylogenetic analysis, because their mode of evolution is predominantly homoplasy-free ..."
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-free and unidirectional. Historically, phylogenetic studies using repetitive elements have relied on biological methods such as PCR analysis. Here, we present a purely computational method for inferring phylogenetic relationships from partial sequence data using orthologous repeats. We apply our method to the phylogeny
Phylogenetic Inference on Cell Processors
, 2008
"... Phylogenetics is a problem in bioinformatics, which requires high performance hardware and fast algorithms to process a constantly increasing amount of data. This thesis addresses both issues by presenting a new search heuristic, called RapidNJ, for the famous Neighbour-Joining method, and by evalua ..."
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, and by evaluating the Playstation 3 Cell processors applicability in distance based phylogenetic inference. RapidNJ significantly reduces the execution time of the Neighbour-Joining method and makes construction of large phylogenetic trees feasible. Experiments are presented, which show that RapidNJ outperforms
Faster Phylogenetic Inference with MXG
"... Abstract. We apply the logic-based declarative programming approach of Model Expansion (MX) to a phylogenetic inference task. We axiomatize the task in multi-sorted first-order logic with cardinality constraints. Using the model expansion solver MXG and SAT+cardinality solver MXC, we compare the per ..."
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Abstract. We apply the logic-based declarative programming approach of Model Expansion (MX) to a phylogenetic inference task. We axiomatize the task in multi-sorted first-order logic with cardinality constraints. Using the model expansion solver MXG and SAT+cardinality solver MXC, we compare
Parallel Phylogenetic Inference
, 2000
"... Recent advances in DNA sequencing technology have created large data sets upon which phylogenetic inference can be performed. However, current research is limited by the prohibitive time necessary to perform tree search on even a reasonably sized data set. Some parallel algorithms have been develope ..."
Abstract
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Cited by 3 (0 self)
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Recent advances in DNA sequencing technology have created large data sets upon which phylogenetic inference can be performed. However, current research is limited by the prohibitive time necessary to perform tree search on even a reasonably sized data set. Some parallel algorithms have been
Probabilism and Phylogenetic Inference
, 1997
"... The maximum likelihood approach to phylogenetics rests on frequency probability theory. This stands in stark contrast to the logical probability of corroboration-based cladistic parsimony. History is particular and cannot be described in terms of universal statements about abstract generalities, the ..."
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Cited by 14 (5 self)
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The maximum likelihood approach to phylogenetics rests on frequency probability theory. This stands in stark contrast to the logical probability of corroboration-based cladistic parsimony. History is particular and cannot be described in terms of universal statements about abstract generalities
Phylogenetic Inference for Multidomain Proteins
, 2011
"... For Mom and Dad. Without your unending support and encouragement, this would not have been possible. iii In this thesis, I present a model of multidomain evolution with associated algorithms and software for phylogenetic analysis of multidomain families, as well as applications of this novel methodo ..."
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For Mom and Dad. Without your unending support and encouragement, this would not have been possible. iii In this thesis, I present a model of multidomain evolution with associated algorithms and software for phylogenetic analysis of multidomain families, as well as applications of this novel
Results 1 - 10
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2,417
