Phylogenetics
By Cambridge University
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Episodes: 126
Description
Phylogenetics is the reconstruction and analysis of trees and networks to describe and understand the evolution of species, populations and individuals. It is widely used in molecular biology and other areas of classification (such as linguistics), and has both led to and benefited from the development of new mathematical, statistical and computational techniques. Although the foundations of phylogenetics were laid down many decades ago, it is currently experiencing an exciting renaissance due to the wealth and types of biological data that are now becoming available. This programme will bring together key researchers in phylogenetics and related areas to further develop this important area of mathematical biology.
The main themes that will be worked on during this programme are new data types in phylogenetics; modelling reticulate evolution; constructing large trees; probabilistic models of evolution; and phylogenetic combinatorics. These themes provide a rich source of mathematical problems in areas such as combinatorics, graph theory, probability theory, topology, and algebraic geometry. Solutions to these problems will provide new insights to questions that are central to contemporary evolutionary biology.
EVENTS:
- Spitalfields Day - Yggdrasil: Reconstructing the Tree of Life
http://www.newton.ac.uk/programmes/PLG/PLG_Spitalfields.html
- Current Challenges and Problems in Phylogenetics
http://www.newton.ac.uk/programmes/PLG/plgw01.html
- Future Directions in Phylogenetic Methods and Models
http://www.newton.ac.uk/programmes/PLG/plgw03.html
- Phylogenetics: New data, new Phylogenetic challenges
http://www.newton.ac.uk/programmes/PLG/plgw05.html
| Episode | Date |
|---|---|
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Estimating ultra-large phylogenies and alignments
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Jun 28, 2011 |
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The combinatorics of distance-based tree inference
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Jun 28, 2011 |
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Assessing the limits of phylogenomics: can too much data be a bad thing?
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Jun 27, 2011 |
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Stochastic Errors vs. Modeling Errors in Distance Based Phylogenetic Reconstructions
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Jun 27, 2011 |
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Integrative analysis if environmental sequences
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Jun 27, 2011 |
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Mammalian phylogeny reveals recent diversi cation rate shifts
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Jun 27, 2011 |
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A generalization of Stirling numbers and distribution of phylogenetic trees
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Jun 27, 2011 |
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A Lie algebraic classification of continuous-time Markov models
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Jun 27, 2011 |
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Tree reconciliations: beyond the LCA mapping
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Jun 27, 2011 |
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Coalescent-based Species Tree Inference from Gene Tree Topologies Under Incomplete Lineage Sorting by Maximum Likelihood
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Jun 27, 2011 |
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Speciation & Extinction Rate Estimation from Phylogenetic Trees
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Jun 27, 2011 |
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Trees as representations of evolutionary information worth keeping
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Jun 27, 2011 |
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Are there alternatives to handling site-to-site rate variation in evolutionary characters
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Jun 27, 2011 |
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An empirical study of the effect of sequence alignment on phylogenetic analysis
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Jun 27, 2011 |
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Modelling protein evolution
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Jun 27, 2011 |
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Sequence Classification using Reference Taxonomies
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Jun 24, 2011 |
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Evaluating the goodness of fit between a phylogenetic model and an alignment
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Jun 24, 2011 |
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Phylodynamic inference - accounting for the interaction of evolutionary and ecological processes
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Jun 24, 2011 |
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Genome sequencing of Leishmania donovani clinical lines reveals dynamic phylogenetic variation
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Jun 24, 2011 |
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New methods of identifying fast-evolving sites in aligned sequence data
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Jun 24, 2011 |
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Principal components analysis in tree space
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Jun 24, 2011 |
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Modeling the Evolutionary Dynamics of CRISPR spacers
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Jun 24, 2011 |
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Corrections to a class of methods for inferring species trees from gene trees
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Jun 24, 2011 |
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Phylogenies from DArTs: A stochastic Dollo proces with censored data
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Jun 23, 2011 |
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Phylogenetic trees and k-dissimilarity maps
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Jun 23, 2011 |
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Reconstructing the parameters of a network from its tree-average distances
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Jun 23, 2011 |
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Visualizing reticulate evolution with planar split networks
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Jun 23, 2011 |
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Tanglegrams for Rooted Phylogenetic Trees and Networks
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Jun 23, 2011 |
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On the elusivity of softwired clusters
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Jun 23, 2011 |
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Reconciling Gene Trees in the Presence of Incomplete Lineage Sorting and Hybridization
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Jun 23, 2011 |
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Quartets and unrooted phylogenetic networks
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Jun 23, 2011 |
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Quantifying diversity and abundance in soil microbial communities from high-throughput sequence data
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Jun 23, 2011 |
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Concordance between species trees and gene trees with multiple mergers of ancestral lineages
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Jun 23, 2011 |
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Exploring Treespace
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Jun 23, 2011 |
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Identifying Lateral Transfers with Neighbor-Nets
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Jun 23, 2011 |
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Metrics on Multi-labeled Trees: Interrelationships and Diameter Bounds
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Jun 23, 2011 |
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On the Complexity of the Quartet Challenge
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Jun 23, 2011 |
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Revisiting the question how many characters are needed to reconstruct the true tree
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Jun 23, 2011 |
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The Complexity of the uSPR distance
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Jun 23, 2011 |
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Recent Progress on Multi-State Perfect Phylogeny (Compatibility) Problems
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Jun 23, 2011 |
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A genealogical approach to studying asexuality
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Jan 16, 2008 |
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Lineage sorting and multi-species coalescent models
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Jan 16, 2008 |
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Incomplete lineage sorting: consistent phylogeny estimation from multiple loci
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Jan 16, 2008 |
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Minimum common supergraphs and haplotype networks
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Jan 16, 2008 |
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The influence of effective population size on a genome-wide positive selection scan
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Jan 16, 2008 |
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Coalescent consequences for consensus cladograms
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Jan 15, 2008 |
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Selecting genomes for reconstruction of ancestral genomes
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Jan 15, 2008 |
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On the optimality of the neighbour-joining algorithm
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Jan 15, 2008 |
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Reconstruction of certain phylogenetic networks from the genomes at leaves
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Jan 15, 2008 |
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A simple model for a complex world
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Jan 15, 2008 |
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Untangling tanglegrams
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Jan 15, 2008 |
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Markov models of protein evolution: Lets get real!
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Jan 15, 2008 |
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Evolution of Chloroplasts
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Jan 15, 2008 |
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Hybridisation in non-binary trees
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Jan 14, 2008 |
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Phylogenetic networks
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Jan 14, 2008 |
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A phylogenetic definition of structure and further animations on the sequence space
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Jan 14, 2008 |
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MIP models for phylenetic reconstruction under minimum evolution
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Jan 14, 2008 |
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10 Men and 1 woman?
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Jan 14, 2008 |
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Ranked tree shapes, shuffles, and a new test for neutrality
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Jan 12, 2008 |
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Distribution of phylogenetic diversity under random extinction
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Jan 12, 2008 |
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Some broad questions about the tree of life
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Jan 11, 2008 |
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On (k.l)-leaf powers
|
Jan 11, 2008 |
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Identifying Phylogenies: extending the notion of unique
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Jan 11, 2008 |
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The identifyability of matrix parameters for covarion-like models
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Jan 11, 2008 |
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Practical distance computation in the space of phylogenetic trees
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Jan 11, 2008 |
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Encoding phylogenetic trees with weighted quartets
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Jan 11, 2008 |
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An exact algorithm for computing the geodesic distance between phylogenetic trees
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Jan 11, 2008 |
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Optimal realisations
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Jan 11, 2008 |
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Phylogenetics of medieval manuscripts
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Jan 11, 2008 |
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Recent progress in phylogenetic combinatorics
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Jan 10, 2008 |
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Optimising phylogenetic diversity across two trees
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Jan 10, 2008 |
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The deep phylogeny problem and its consequences
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Jan 10, 2008 |
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On the hardness of inferring Phylogenies from triplet-dissimilarities
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Jan 10, 2008 |
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On the nature of heterotachy
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Jan 10, 2008 |
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A signal-to-noise analysis of phylogeny estimation by neighbour-joining
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Jan 10, 2008 |
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Adaptive fast convergence - towards optimal reconstruction guarantees for Phylogenetic trees
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Jan 10, 2008 |
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Incorporating uncertainty in distance-matrix phylogenetic reconstruction
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Jan 10, 2008 |
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How many characters are needed to recontruct the true tree?
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Jan 10, 2008 |
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Performance of new invariant methods for phylogenetic reconstuction
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Jan 10, 2008 |
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Seeing the wood for trees: analysing multiple alternative phylogenies
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Dec 18, 2007 |
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The tree of life: algorithmic and software challenges
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Dec 17, 2007 |
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Phylogenetic combinatorics: analysing branching patterns in evolutionary trees
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Dec 13, 2007 |
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Phylogenetic models and algebra
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Dec 13, 2007 |
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Algorithm design for large-scale phylogenetic analysis
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Dec 13, 2007 |
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Phylogenetic models and the origins of chloroplasts
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Dec 13, 2007 |
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New methods for estimating language evolution
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Dec 11, 2007 |
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Hao Bailin's whole-genome based phylogenies
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Dec 11, 2007 |
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Constructing level-2 phylogenetic trees from triplets
|
Dec 10, 2007 |
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Phylogenetics: interactions between mathematics and evolution
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Nov 28, 2007 |
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Optimal and hereditarily optimal realisation of metric spaces
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Oct 01, 2007 |
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Mapping human genetic ancestry
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Sep 27, 2007 |
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Stars, nets, and the "war on error": Six mathematical challenges
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Sep 27, 2007 |
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Properties of the TBR metric
|
Sep 27, 2007 |
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Consistency of phylogenetic tree search algorithms based on the balanced minimum evolution principle
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Sep 27, 2007 |
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Generalising from consensus to supertree methods
|
Sep 25, 2007 |
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Computing phylogenetic diversity for split systems
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Sep 25, 2007 |
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Nature reserve selection problems
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Sep 24, 2007 |
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Big trees: challenges and opportunites in the phylogenetic analysis of large data sets
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Sep 24, 2007 |
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Model averaging in phylogenies
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Sep 24, 2007 |
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Neighbor joining algorithms for inferring phylogenies via LCA-distances
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Sep 24, 2007 |
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Glimpses from the strange world of phylogenetic mixtures
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Sep 21, 2007 |
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Prioritising species for biodoversity conservation
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Sep 21, 2007 |
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Reconstruction of phylogenetic trees with very short branches
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Sep 20, 2007 |
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Indentifiability of the GTR=gamma substitution model of DNA evolution
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Sep 20, 2007 |
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Likelihood calculations on the ancestral recombination graph
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Sep 19, 2007 |
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Insertion-deletion models for dequence evolution and Bayesian sampling methods for multiple alignment
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Sep 14, 2007 |
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Explicit bounds for the stability of maximum likelihood trees
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Sep 13, 2007 |
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Partitioning the sample space on five taxa for the neighbour joining algorithm
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Sep 13, 2007 |
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New analytical results for the speciation times in neutral models
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Sep 13, 2007 |
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Branch and bound construction of balanced minimum evolution optimal trees
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Sep 13, 2007 |
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On k-leaf powers
|
Sep 12, 2007 |
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Integer programming for phylogenetic computations
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Sep 12, 2007 |
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Maximum parsimony on phylogenetic networks: some rigorous results
|
Sep 11, 2007 |
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Inference rules for super-network construction
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Sep 11, 2007 |
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Computational and mathematical challenges involved in very large-scale phylogenetics
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Sep 11, 2007 |
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Advances and limitations of maximum likelihood phylogenetics
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Sep 11, 2007 |
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Restrictions on meaningful phylogenetic networks
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Sep 11, 2007 |
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Quartet compatability: new results and surprising counter-examples
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Sep 11, 2007 |
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Dendroscope - an interactive viewer for large phylogenetic trees
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Sep 07, 2007 |
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Appropriate models for heterogeneous multi-gene data sites
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Sep 07, 2007 |
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Incorporating speices phylogeny in the reconstruction of gene trees
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Sep 06, 2007 |
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Mixture models in phylogenetic inference
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Sep 06, 2007 |
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Comparing phylogenetic trees
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Sep 06, 2007 |
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Phylogenetic reconstructions based on RNA secondary structure
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Sep 06, 2007 |
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Tripartitions in phylogenetic networks
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Sep 05, 2007 |
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Reconstruction of phylogeny by stratophenetic tracing in the fossil record and its comparison with molecular data
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Sep 05, 2007 |