cipres_all_12_1_2007.enlEndNote11117<style face="normal" font="default" size="100%">The prior and the posterior in Bayesian phylogenetics</style>cipres_all_12_1_2007.enlEndNote11217<style face="normal" font="default" size="100%">Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty</style>cipres_all_12_1_2007.enlEndNote11317<style face="normal" font="default" size="100%">Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference</style>cipres_all_12_1_2007.enlEndNote11417<style face="normal" font="default" size="100%">Efficient enumeration of phylogenetically informative substrings</style>cipres_all_12_1_2007.enlEndNote11517<style face="normal" font="default" size="100%">Genome identification and classification by short oligo arrays</style>cipres_all_12_1_2007.enlEndNote11717<style face="normal" font="default" size="100%">Lower bounds for maximum parsimony with gene order data</style>cipres_all_12_1_2007.enlEndNote717<style face="normal" font="default" size="100%">Computational biology and high-performance computing </style>cipres_all_12_1_2007.enlEndNote517<style face="normal" font="default" size="100%">An improved, randomized algorithm for parallel selection with an experimental study</style>cipres_all_12_1_2007.enlEndNote1105<style face="normal" font="default" size="100%">High-performance algorithm engineering for large-scale graph problems and computational biology</style>cipres_all_12_1_2007.enlEndNote11810<style face="normal" font="default" size="100%">ExactMP: An efficient parallel exact solver for phylogenetic tree reconstruction using maximum parsimony. </style>cipres_all_12_1_2007.enlEndNote3010<style face="normal" font="default" size="100%">Fast shared memory algorithms for computing the minimum spanning forest of sparse graphs</style>cipres_all_12_1_2007.enlEndNote12017<style face="normal" font="default" size="100%">Fast shared-memory algorithms for graph theoretic problems</style>cipres_all_12_1_2007.enlEndNote1195<style face="normal" font="default" size="100%">Efficient parallel graph algorithms for shared-memory multiprocessors. </style>cipres_all_12_1_2007.enlEndNote12110<style face="normal" font="default" size="100%">On the Architectural Requirements for Efficient Execution of Graph Algorithms</style>cipres_all_12_1_2007.enlEndNote10617<style face="normal" font="default" size="100%">A fast, parallel spanning tree algorithm for symmetric multiprocessors (SMPS)</style>cipres_all_12_1_2007.enlEndNote525<style face="normal" font="default" size="100%">Parallel algorithm design for branch and bound</style>cipres_all_12_1_2007.enlEndNote24410<style face="normal" font="default" size="100%">BioPerf: A Benchmark Suite to Evaluate High-Performance Computer Architecture on Bioinformatics Applications</style>cipres_all_12_1_2007.enlEndNote5010<style face="normal" font="default" size="100%">A parallel state assignment algorithm for finite state machines </style>cipres_all_12_1_2007.enlEndNote12210<style face="normal" font="default" size="100%">Design and implementation of the HPCS graph analysis benchmark on symmetric multiprocessors.</style>cipres_all_12_1_2007.enlEndNote12310<style face="normal" font="default" size="100%">Designing Multithreaded Algorithms for Breadth-First Search and st-connectivity on the Cray MTA-2</style>cipres_all_12_1_2007.enlEndNote12410<style face="normal" font="default" size="100%">Parallel Algorithms for Evaluating Centrality Indices in Real-world Networks</style>cipres_all_12_1_2007.enlEndNote1255<style face="normal" font="default" size="100%">Design of multithreaded algorithms for combinatorial problems</style>cipres_all_12_1_2007.enlEndNote12610<style face="normal" font="default" size="100%">Computational grand challenges in assembling the tree of life: Problems & solutions</style>cipres_all_12_1_2007.enlEndNote1275<style face="normal" font="default" size="100%">Computational Grand Challenges in Assembling the Tree of Life: Problems & Solutions</style>cipres_all_12_1_2007.enlEndNote12810<style face="normal" font="default" size="100%">A Cache-Aware Parallel Implementation of the Push-Relabel Network Flow Algorithm and Experimental Evaluation of the Gap Relabeling Heuristic</style>cipres_all_12_1_2007.enlEndNote1295<style face="normal" font="default" size="100%">High Performance Algorithms for Phylogeny Reconstruction with Maximum Parsimony</style>cipres_all_12_1_2007.enlEndNote13010<style face="normal" font="default" size="100%">Reconstructing strings from random traces</style>cipres_all_12_1_2007.enlEndNote10017<style face="normal" font="default" size="100%">Dating the dipsacales: Comparing models, genes, and evolutionary implications</style>cipres_all_12_1_2007.enlEndNote8817<style face="normal" font="default" size="100%">Phylogeny and biogeography of Valerianaceae (Dipsacales) with special reference to the South American valerians</style>cipres_all_12_1_2007.enlEndNote1440<style face="normal" font="default" size="100%">Properties of compatibility and consensus sets of phylogenetic trees </style>cipres_all_12_1_2007.enlEndNote2210<style face="normal" font="default" size="100%">Online consensus of phylogenetic trees</style>cipres_all_12_1_2007.enlEndNote24317<style face="normal" font="default" size="100%">The delayed rise of present-day mammals</style>cipres_all_12_1_2007.enlEndNote1315<style face="normal" font="default" size="100%">A model for user-oriented data provenance in pipelined scientific workflows</style>cipres_all_12_1_2007.enlEndNote13210<style face="normal" font="default" size="100%">A compressed format for collections of phylogenetic trees and improved consensus performance.</style>cipres_all_12_1_2007.enlEndNote13317<style face="normal" font="default" size="100%">MAVID: constrained ancestral alignment of multiple sequences</style>cipres_all_12_1_2007.enlEndNote13410<style face="normal" font="default" size="100%">On the tandem duplication-random loss model of genome rearrangement. </style>cipres_all_12_1_2007.enlEndNote13517<style face="normal" font="default" size="100%">HSP90 family of genes in the human genome: insights into their divergence and evolution </style>cipres_all_12_1_2007.enlEndNote13617<style face="normal" font="default" size="100%">Bioinformatics for whole-genome shotgun sequencing of microbial communities</style>cipres_all_12_1_2007.enlEndNote13717<style face="normal" font="default" size="100%">Maximum likelihood Jukes-Cantor triples: Analytical solutions. </style>cipres_all_12_1_2007.enlEndNote13817<style face="normal" font="default" size="100%">Molecular clock forks: Symbolic mathematical analysis.</style>cipres_all_12_1_2007.enlEndNote9917<style face="normal" font="default" size="100%">John H. Beaman - Recipient of the 2004 Asa Gray Award</style>cipres_all_12_1_2007.enlEndNote13910<style face="normal" font="default" size="100%">PRec-I-DCM3: A parallel framework for fast and accurate large scale phylogeny reconstruction. </style>cipres_all_12_1_2007.enlEndNote1405<style face="normal" font="default" size="100%">Towards a model of provenance and user views in scientific workflows.</style>cipres_all_12_1_2007.enlEndNote1055<style face="normal" font="default" size="100%">A user-centric framework for accessing biological sources and tools</style>cipres_all_12_1_2007.enlEndNote810<style face="normal" font="default" size="100%">The Euler tour technique and parallel rooted spanning tree</style>cipres_all_12_1_2007.enlEndNote5110<style face="normal" font="default" size="100%">Lock-free parallel algorithms: an experimental study </style>cipres_all_12_1_2007.enlEndNote14110<style face="normal" font="default" size="100%">An empirical analysis of parallel random permutation algorithms on smps.</style>cipres_all_12_1_2007.enlEndNote14217<style face="normal" font="default" size="100%">Designing irregular parallel algorithms with mutual exclusion and lock-free protocols. </style>cipres_all_12_1_2007.enlEndNote1436<style face="normal" font="default" size="100%">Assembling the Tree of Life</style>cipres_all_12_1_2007.enlEndNote14417<style face="normal" font="default" size="100%">Adaptive evolution of chloroplast genome structure. </style>cipres_all_12_1_2007.enlEndNote1455<style face="normal" font="default" size="100%">Maximal accurate forests from distance matrices. </style>cipres_all_12_1_2007.enlEndNote14610<style face="normal" font="default" size="100%">Optimal Phylogenetic Reconstruction</style>cipres_all_12_1_2007.enlEndNote14710<style face="normal" font="default" size="100%">Efficiently supporting structure queries on phylogenetic trees</style>cipres_all_12_1_2007.enlEndNote9717<style face="normal" font="default" size="100%">Explosive radiation of malpighiales supports a mid-Cretaceous origin of modern tropical rain forests</style>cipres_all_12_1_2007.enlEndNote1485<style face="normal" font="default" size="100%">Comparisons, phylogeny, and teaching evolution</style>cipres_all_12_1_2007.enlEndNote8917<style face="normal" font="default" size="100%">Key innovations, convergence, and success: macroevolutionary lessons from plant phylogeny</style>cipres_all_12_1_2007.enlEndNote15017<style face="normal" font="default" size="100%">Viburnum phylogeny based on chloroplast trnK intron and nuclear ribosomal ITS DNA sequences</style>cipres_all_12_1_2007.enlEndNote14917<style face="normal" font="default" size="100%">Implementing the PhyloCode</style>cipres_all_12_1_2007.enlEndNote1515<style face="normal" font="default" size="100%">Biodiversity inventory: Reflections on preparedness and efficiency</style>cipres_all_12_1_2007.enlEndNote15217<style face="normal" font="default" size="100%">PRec-I-DCM3: A parallel framework for fast and accurate large scale phylogeny reconstruction</style>cipres_all_12_1_2007.enlEndNote15310<style face="normal" font="default" size="100%">Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood. </style>cipres_all_12_1_2007.enlEndNote10817<style face="normal" font="default" size="100%">Reconstruction of large phylogenetic trees: A parallel approach</style>cipres_all_12_1_2007.enlEndNote9517<style face="normal" font="default" size="100%">Genetic diversity in Chihuahuan Desert populations of creosotebush (Zygophyllaceae : Larrea tridentata)</style>cipres_all_12_1_2007.enlEndNote2410<style face="normal" font="default" size="100%">Reversing gene erosion: Reconstructing ancestral bacterial genomes from gene-content and order data</style>cipres_all_12_1_2007.enlEndNote15410<style face="normal" font="default" size="100%">PILER: Identification and classification of repeated genomic elements.</style>cipres_all_12_1_2007.enlEndNote8717<style face="normal" font="default" size="100%">Basal cactus phylogeny: Implications of Pereskia (Cactaceae) paraphyly for the transition to the cactus life form</style>cipres_all_12_1_2007.enlEndNote2455<style face="normal" font="default" size="100%">Tree construction using singular value decomposition</style>cipres_all_12_1_2007.enlEndNote15510<style face="normal" font="default" size="100%">The homology kernel: A biologically motivated sequence embedding into Euclidean space</style>cipres_all_12_1_2007.enlEndNote15617<style face="normal" font="default" size="100%">Incorporating homologues into sequence embeddings for protein analysis.</style>cipres_all_12_1_2007.enlEndNote7817<style face="normal" font="default" size="100%">Unidentifiable divergence times in rates-across-sites models</style>cipres_all_12_1_2007.enlEndNote1575<style face="normal" font="default" size="100%">Inference of divergence times as a statistical inverse problem</style>cipres_all_12_1_2007.enlEndNote15817<style face="normal" font="default" size="100%">Dark and disturbed: a new image of early angiosperm ecology</style>cipres_all_12_1_2007.enlEndNote1595<style face="normal" font="default" size="100%">Pattern identification in biogeography: metrics and algorithms for comparing area cladograms</style>cipres_all_12_1_2007.enlEndNote7210<style face="normal" font="default" size="100%">Better Hill-Climbing Seaches for Parsimony</style>cipres_all_12_1_2007.enlEndNote7410<style face="normal" font="default" size="100%">On Contract-and-Refine-Transformations Between Phylogenetic Trees</style>cipres_all_12_1_2007.enlEndNote16017<style face="normal" font="default" size="100%">The cobweb of life revealed by genome-scale estimates of horizontal gene transfer</style>cipres_all_12_1_2007.enlEndNote16117<style face="normal" font="default" size="100%">Bayesian inference of the metazoan phylogeny: A combined analysis. </style>cipres_all_12_1_2007.enlEndNote10117<style face="normal" font="default" size="100%">Phylogenetic analysis of Trechitae (Coleoptera : Carabidae) based on larval morphology, with a description of first-instar Phrypeus and a key to genera</style>cipres_all_12_1_2007.enlEndNote16210<style face="normal" font="default" size="100%">Authentication framework in the Kepler workflow system. </style>cipres_all_12_1_2007.enlEndNote16317<style face="normal" font="default" size="100%">Modeling the site-specific variation of selection patterns along lineages</style>cipres_all_12_1_2007.enlEndNote16410<style face="normal" font="default" size="100%">Approximating the best-fit tree under Lp norms</style>cipres_all_12_1_2007.enlEndNote16517<style face="normal" font="default" size="100%">BIO-AJAX: An extensible framework for biological data cleaning. </style>cipres_all_12_1_2007.enlEndNote16610<style face="normal" font="default" size="100%">Lineage path integration for phylogenetic resources</style>cipres_all_12_1_2007.enlEndNote8617<style face="normal" font="default" size="100%">Analysis and visualization of tree space</style>cipres_all_12_1_2007.enlEndNote10317<style face="normal" font="default" size="100%">Phylogeny of the New World true frogs (Rana)</style>cipres_all_12_1_2007.enlEndNote16717<style face="normal" font="default" size="100%">Hastings ratio of the LOCAL proposal used in Bayesian phylogenet¬ics</style>cipres_all_12_1_2007.enlEndNote9217<style face="normal" font="default" size="100%">Duplications in CYC-like genes from dipsacales correlate with floral form</style>cipres_all_12_1_2007.enlEndNote16817<style face="normal" font="default" size="100%">Bayesian phylogenetic model selection using reversible jump Markov Chain Monte Carlo.</style>cipres_all_12_1_2007.enlEndNote16917<style face="normal" font="default" size="100%">Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models.</style>cipres_all_12_1_2007.enlEndNote1705<style face="normal" font="default" size="100%">Bayesian analysis of molecular evolution using MrBayes</style>cipres_all_12_1_2007.enlEndNote17117<style face="normal" font="default" size="100%">Robust reconstruction on trees is determined by the second eigenvalue.</style>cipres_all_12_1_2007.enlEndNote17210<style face="normal" font="default" size="100%">Efficient parsimony-based methods for phylogenetic network reconstruction</style>cipres_all_12_1_2007.enlEndNote24017<style face="normal" font="default" size="100%">Maximum Likelihood of Phylogenetic Networks</style>cipres_all_12_1_2007.enlEndNote1735<style face="normal" font="default" size="100%">Reconstructing evolution of natural languages: Complexity and parameterized algorithms</style>cipres_all_12_1_2007.enlEndNote17410<style face="normal" font="default" size="100%">More on reconstructing strings from random traces: Insertions and deletions</style>cipres_all_12_1_2007.enlEndNote435<style face="normal" font="default" size="100%">Inferring phylogeny using genomic characters: a case study using land plant plastomes </style>cipres_all_12_1_2007.enlEndNote11617<style face="normal" font="default" size="100%">Maximum likelihood on molecular clock comb: Analytic solutions. </style>cipres_all_12_1_2007.enlEndNote17517<style face="normal" font="default" size="100%">Hyphy: A platform for molecular evolutionary analysis. </style>cipres_all_12_1_2007.enlEndNote17617<style face="normal" font="default" size="100%">Modeling heterogeneity of synonymous and nonsynonymous substitution rates across sites</style>cipres_all_12_1_2007.enlEndNote23917<style face="normal" font="default" size="100%">The 2006 NESCent Phyloinformatics Hackathon: A Field Report</style>cipres_all_12_1_2007.enlEndNote9117<style face="normal" font="default" size="100%">Polytomies and Bayesian phylogenetic inference</style>cipres_all_12_1_2007.enlEndNote17717<style face="normal" font="default" size="100%">Network (reticulated) evolution: Biology, models, and algorithms</style>cipres_all_12_1_2007.enlEndNote17817<style face="normal" font="default" size="100%">Reconstructing patterns of reticulate evolution in plants. </style>cipres_all_12_1_2007.enlEndNote1795<style face="normal" font="default" size="100%">An overview of phylogeny reconstruction.</style>cipres_all_12_1_2007.enlEndNote1805<style face="normal" font="default" size="100%">Quartet methods for phylogeny reconstruction from gene orders. </style>cipres_all_12_1_2007.enlEndNote18117<style face="normal" font="default" size="100%">Extensive site-to-site variability of synonymous substitution rates in mitochondrial genomes</style>cipres_all_12_1_2007.enlEndNote18210<style face="normal" font="default" size="100%">On optimizing distance-based similarity search for biological databases</style>cipres_all_12_1_2007.enlEndNote2517<style face="normal" font="default" size="100%">Genomic distances under deletions and insertions</style>cipres_all_12_1_2007.enlEndNote1835<style face="normal" font="default" size="100%">Parametric inference</style>cipres_all_12_1_2007.enlEndNote18410<style face="normal" font="default" size="100%">Why neighbor-joining works</style>cipres_all_12_1_2007.enlEndNote410<style face="normal" font="default" size="100%">BLOG: Relational modeling with unknown objects</style>cipres_all_12_1_2007.enlEndNote310<style face="normal" font="default" size="100%">Approximate inference for infinite contingent Bayesian networks</style>cipres_all_12_1_2007.enlEndNote18510<style face="normal" font="default" size="100%">MoBIoS: A metric-space DBMS to support biological discovery</style>cipres_all_12_1_2007.enlEndNote8217<style face="normal" font="default" size="100%">The evolution and ecology of desiccation tolerance in mosses</style>cipres_all_12_1_2007.enlEndNote25<style face="normal" font="default" size="100%">The logic of the data matrix in phylogenetic analysis</style>cipres_all_12_1_2007.enlEndNote1865<style face="normal" font="default" size="100%">Detecting diversification rate variation in supertrees.</style>cipres_all_12_1_2007.enlEndNote18717<style face="normal" font="default" size="100%">Increasing data transparency and estimating phylogenetic uncertainty in supertrees: Approaches using nonparametric bootstrapping. </style>cipres_all_12_1_2007.enlEndNote18817<style face="normal" font="default" size="100%">Incorporating fossil data in biogeographic inference: a likelihood approach</style>cipres_all_12_1_2007.enlEndNote1895<style face="normal" font="default" size="100%">Using semi-definite programming to enhance supertree resolvability</style>cipres_all_12_1_2007.enlEndNote19010<style face="normal" font="default" size="100%">Convex recolorings of strings and trees: Definitions, hardness results and algorithms</style>cipres_all_12_1_2007.enlEndNote1910<style face="normal" font="default" size="100%">Computational challenges from the Tree of Life</style>cipres_all_12_1_2007.enlEndNote985<style face="normal" font="default" size="100%">High-performance algorithm engineering for computational phylogenetics</style>cipres_all_12_1_2007.enlEndNote6517<style face="normal" font="default" size="100%">Phylogenetic networks: modeling, reconstructibility, and accuracy</style>cipres_all_12_1_2007.enlEndNote185<style face="normal" font="default" size="100%">Reconstructing phylogenies from gene-content and gene-order data</style>cipres_all_12_1_2007.enlEndNote855<style face="normal" font="default" size="100%">Advances in phylogeny reconstruction from gene order and content data</style>cipres_all_12_1_2007.enlEndNote19117<style face="normal" font="default" size="100%">NetGen: Generating phylogenetic networks with diploid hybrids</style>cipres_all_12_1_2007.enlEndNote19217<style face="normal" font="default" size="100%">Phase transitions in phylogeny</style>cipres_all_12_1_2007.enlEndNote1935<style face="normal" font="default" size="100%">Survey: Information flow on trees.</style>cipres_all_12_1_2007.enlEndNote19417<style face="normal" font="default" size="100%">Distorted metrics on trees and phylogenetic forests</style>cipres_all_12_1_2007.enlEndNote19717<style face="normal" font="default" size="100%">A phase transition for a random cluster model on phylogenetic trees</style>cipres_all_12_1_2007.enlEndNote19510<style face="normal" font="default" size="100%">Learning Nonsingular Phylogenies and Hidden Markov Models</style>cipres_all_12_1_2007.enlEndNote19617<style face="normal" font="default" size="100%">Learning nonsingular phylogenies and Hidden Markov Models</style>cipres_all_12_1_2007.enlEndNote1985<style face="normal" font="default" size="100%">How much can evolved characters tell us about the tree that generated them?</style>cipres_all_12_1_2007.enlEndNote19917<style face="normal" font="default" size="100%">Limitations of Markov Chain Monte Carlo Algorithms for Bayesian Inference of Phylogeny Science. </style>cipres_all_12_1_2007.enlEndNote20017<style face="normal" font="default" size="100%">Limitations of Markov Chain Monte Carlo algorithms for Bayesian inference of phylogeny. </style>cipres_all_12_1_2007.enlEndNote1540<style face="normal" font="default" size="100%">Quality measures for phylogenetic networks</style>cipres_all_12_1_2007.enlEndNote20110<style face="normal" font="default" size="100%">Reconstructing phylogenetic networks using maximum parsimony</style>cipres_all_12_1_2007.enlEndNote7717<style face="normal" font="default" size="100%">Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages.</style>cipres_all_12_1_2007.enlEndNote2025<style face="normal" font="default" size="100%">Gene trees, species trees, and species networks</style>cipres_all_12_1_2007.enlEndNote2035<style face="normal" font="default" size="100%">RIATA-HGT: A fast and accurate heuristic for reconstructing horizontal gene transfer</style>cipres_all_12_1_2007.enlEndNote2045<style face="normal" font="default" size="100%">Phylogenetic networks: Properties and relationship to trees and clusters. </style>cipres_all_12_1_2007.enlEndNote1095<style face="normal" font="default" size="100%">Phylogenetic networks, trees, and clusters</style>cipres_all_12_1_2007.enlEndNote10717<style face="normal" font="default" size="100%">Reconstructing reticulate evolution in species - Theory and practice</style>cipres_all_12_1_2007.enlEndNote7917<style face="normal" font="default" size="100%">A Comparison of Phylogenetic Reconstruction Methods on an IE Dataset</style>cipres_all_12_1_2007.enlEndNote20517<style face="normal" font="default" size="100%">Reconstructing trees from subtree weights</style>cipres_all_12_1_2007.enlEndNote20617<style face="normal" font="default" size="100%">Efficiently computing the Robinson-Foulds metric</style>cipres_all_12_1_2007.enlEndNote2075<style face="normal" font="default" size="100%">A sublinear-time randomized approximation scheme for the Robinson-Foulds metric</style>cipres_all_12_1_2007.enlEndNote20817<style face="normal" font="default" size="100%">A likelihood framework for inferring the evolution of geographic range on phylogenetic trees</style>cipres_all_12_1_2007.enlEndNote20917<style face="normal" font="default" size="100%">A short proof that phylogenetic tree reconstruction by maximum likelihood is hard</style>cipres_all_12_1_2007.enlEndNote21010<style face="normal" font="default" size="100%"> Improving phylogenetic motif prediction using parsimony</style>cipres_all_12_1_2007.enlEndNote275<style face="normal" font="default" size="100%">Performance of supertree methods on various dataset decompositions</style>cipres_all_12_1_2007.enlEndNote21110<style face="normal" font="default" size="100%">Rec-I-DCM3: A fast algorithmic technique for reconstructing large phylogenetic trees</style>cipres_all_12_1_2007.enlEndNote3110<style face="normal" font="default" size="100%">Rec-I-DCM3: A fast algorithmic technique for reconstructing phylogenetic trees</style>cipres_all_12_1_2007.enlEndNote21217<style face="normal" font="default" size="100%">Recombination and phylogeny: effects and detection</style>cipres_all_12_1_2007.enlEndNote21310<style face="normal" font="default" size="100%">RECOMP: A parsimony-based method for detecting recombination.</style>cipres_all_12_1_2007.enlEndNote21410<style face="normal" font="default" size="100%">Techniques for assessing phylogenetic branch support: A performance study</style>cipres_all_12_1_2007.enlEndNote21517<style face="normal" font="default" size="100%">Molecular phylogeny and biogeography of Ribes (Grossulariaceae), with an emphasis on gooseberries (subg. Grossularia). </style>cipres_all_12_1_2007.enlEndNote21617<style face="normal" font="default" size="100%">Multiple alignment by sequence annealing. </style>cipres_all_12_1_2007.enlEndNote21717<style face="normal" font="default" size="100%">A motif-base framework for recognizing sequence families. </style>cipres_all_12_1_2007.enlEndNote6717<style face="normal" font="default" size="100%">A framework for measuring supercomputer productivity</style>cipres_all_12_1_2007.enlEndNote2185<style face="normal" font="default" size="100%">Phylogenetic profiling of insertions and deletions in vertebrate genomes</style>cipres_all_12_1_2007.enlEndNote21910<style face="normal" font="default" size="100%">Performance analysis of parallel programs via message-passing graph traversal</style>cipres_all_12_1_2007.enlEndNote3417<style face="normal" font="default" size="100%">Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining</style>cipres_all_12_1_2007.enlEndNote2205<style face="normal" font="default" size="100%">Biomonitoring, phylogenetics and anomaly aggregation systems</style>cipres_all_12_1_2007.enlEndNote22117<style face="normal" font="default" size="100%">Positively selected sites in the arabidopsis receptor-like kinase gene family</style>cipres_all_12_1_2007.enlEndNote9017<style face="normal" font="default" size="100%">Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation</style>cipres_all_12_1_2007.enlEndNote6110<style face="normal" font="default" size="100%">Approximating the true evolutionary distance between two genomes </style>cipres_all_12_1_2007.enlEndNote22217<style face="normal" font="default" size="100%">Approximating the true evolutionary distance between two genomes</style>cipres_all_12_1_2007.enlEndNote2235<style face="normal" font="default" size="100%">A framework for orthology assignment from gene rearrangement data</style>cipres_all_12_1_2007.enlEndNote1317<style face="normal" font="default" size="100%">Distance correction for large pairwise genomic distances, </style>cipres_all_12_1_2007.enlEndNote2910<style face="normal" font="default" size="100%">Phylogenetic reconstruction from arbitrary gene-order data</style>cipres_all_12_1_2007.enlEndNote22410<style face="normal" font="default" size="100%">Improving genome rearrangement phylogeny using sequence-style parsimony</style>cipres_all_12_1_2007.enlEndNote845<style face="normal" font="default" size="100%">Linear programming for phylogenetic reconstruction based on gene rearrangements</style>cipres_all_12_1_2007.enlEndNote22517<style face="normal" font="default" size="100%">An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data</style>cipres_all_12_1_2007.enlEndNote22617<style face="normal" font="default" size="100%">Comparative metagenomics of microbial communities</style>cipres_all_12_1_2007.enlEndNote375<style face="normal" font="default" size="100%">Distance-based genome rearrangement phylogeny</style>cipres_all_12_1_2007.enlEndNote22717<style face="normal" font="default" size="100%">Reconstructing chromosomal evolution</style>cipres_all_12_1_2007.enlEndNote22817<style face="normal" font="default" size="100%">Distance-based genome rearrangement phylogeny</style>cipres_all_12_1_2007.enlEndNote2295<style face="normal" font="default" size="100%">Large-scale phylogenetic analyses</style>cipres_all_12_1_2007.enlEndNote4217<style face="normal" font="default" size="100%">A stochastic model of language evolution that incorporates homoplasy and borrowing</style>cipres_all_12_1_2007.enlEndNote9617<style face="normal" font="default" size="100%">Phylomatic: tree assembly for applied phylogenetics</style>cipres_all_12_1_2007.enlEndNote23017<style face="normal" font="default" size="100%">Phylodiversity-dependent seedling mortality, size structure, and disease in a Bornean rain forest. </style>cipres_all_12_1_2007.enlEndNote23117<style face="normal" font="default" size="100%">Dynamic homology and the likelihood criterion.</style>cipres_all_12_1_2007.enlEndNote10417<style face="normal" font="default" size="100%">Historical biogeography, ecology and species richness</style>cipres_all_12_1_2007.enlEndNote9317<style face="normal" font="default" size="100%">Absence asymmetry: The evolution of monorchid beetles (Insecta : Coleoptera : Carabidae)</style>cipres_all_12_1_2007.enlEndNote2325<style face="normal" font="default" size="100%">High-performance phylogeny reconstruction under maximum parsi¬mony</style>cipres_all_12_1_2007.enlEndNote1640<style face="normal" font="default" size="100%">The relationship between maximum parsimony scores and phylogenetic tree topologies</style>cipres_all_12_1_2007.enlEndNote23310<style face="normal" font="default" size="100%">Cooperative-Rec-I-DCM3: A population-based approach for reconstructing phylogenies</style>cipres_all_12_1_2007.enlEndNote23410<style face="normal" font="default" size="100%">Phylospaces: Evolutionary trees and tuple space</style>cipres_all_12_1_2007.enlEndNote23510<style face="normal" font="default" size="100%">The role of diverse populations in phylogenetic analysis</style>cipres_all_12_1_2007.enlEndNote9417<style face="normal" font="default" size="100%">Viburnum phylogeny based on combined molecular data: Implications for taxonomy and biogeography</style>cipres_all_12_1_2007.enlEndNote23610<style face="normal" font="default" size="100%"> Using MoBIos scalable genome join to find conserved primer pair candidates between two genomes</style>cipres_all_12_1_2007.enlEndNote24210<style face="normal" font="default" size="100%">A divide-and-conquer implementation of three sequence alignment and ancestor inference.</style>cipres_all_12_1_2007.enlEndNote24117<style face="normal" font="default" size="100%">A space-effecient algorithm for three sequence alignment and ancestor inference (accepted).</style>cipres_all_12_1_2007.enlEndNote23710<style face="normal" font="default" size="100%">PhyloMiner: A Tool for Evolutionary Data Analysis</style>cipres_all_12_1_2007.enlEndNote23810<style face="normal" font="default" size="100%">Crimson: A data management system to support evaluating phylogenetic tree reconstruction algorithms</style>cipres_all_12_1_2007.enlEndNote10217<style face="normal" font="default" size="100%">Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics</style>