The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.

https://bioinformatics.cs.vt.edu/~easychair/HusonBryant_MBE_2006.pdf

Application of Phylogenetic Networks in Evolutionary Studies

BOLD: The Barcode of Life Data System: Barcoding

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement Neighbor-Joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N2) space and O(N2L) time, but FastTree requires just O(NLa + N) memory and O(Nlog (N)La) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 h and 2.4 GB of memory. Just computing pairwise Jukes–Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 h and 50 GB of memory. In simulations, FastTree was slightly more accurate than Neighbor-Joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fasttree-computing-large-minimum-evolution-trees-with-eo2tre5l8r.pdf

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fast-tree-computing-large-minimum-evolution-trees-with-4grq0gwfpy.pdf

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

For a set of points in the plane and a fixed integer $k > 0$, the Yao graph $Y_k$ partitions the space around each point into $k$ equiangular cones of angle $\theta=2\pi/k$, and connects each point to a nearest neighbor in each cone. It is known for all Yao graphs, with the sole exception of $Y_5$, whether or not they are geometric spanners. In this paper we close this gap by showing that for odd $k \geq 5$, the spanning ratio of $Y_k$ is at most $1/(1-2\sin(3\theta/8))$, which gives the first constant upper bound for $Y_5$, and is an improvement over the previous bound of $1/(1-2\sin(\theta/2))$ for odd $k \geq 7$. We further reduce the upper bound on the spanning ratio for $Y_5$ from $10.9$ to $2+\sqrt{3} \approx 3.74$, which falls slightly below the lower bound of $3.79$ established for the spanning ratio of $\Theta_5$ ($\Theta$-graphs differ from Yao graphs only in the way they select the closest neighbor in each cone). This is the first such separation between a Yao and $\Theta$-graph with the same number of cones. We also give a lower bound of $2.87$ on the spanning ratio of $Y_5$. Finally, we revisit the $Y_6$ graph, which plays a particularly important role as the transition between the graphs ($k > 6$) for which simple inductive proofs are known, and the graphs ($k \le 6$) whose best spanning ratios have been established by complex arguments. Here we reduce the known spanning ratio of $Y_6$ from $17.6$ to $5.8$, getting closer to the spanning ratio of 2 established for $\Theta_6$.

New and Improved Spanning Ratios for Yao Graphs

B-trees with relaxed balance have been defined to facilitate first updating on shared-memory asynchronous parallel architectures. To obtain this, rebalancing has been uncoupled from the updating such that extensive locking can be avoided in connection with updates. We analyze B-trees with relaxed balance, and prove that each update gives rise to at most [log/sub a/(N/2)]+1 rebalancing operations, where a is the degree of the B-tree, and N is the bound an its maximal size since it was last in balance. Assuming that the size of nodes are at least twice the degree, we prove that rebalancing can be performed in amortized constant time. So, in the long run, rebalancing is constant time on average, even if any particular update could give rise to logarithmic time rebalancing. We also prove that the amount of rebalancing done at any particular level decreases exponentially going from the leaves towards the root. This is important since the higher up in the tree a lock due to a rebalancing operation occurs, the larger a subtree which cannot be accessed by other processes for the duration of that lock. All of these results are in fact obtained for the more general (a, b)-trees, so we have results for both of the common B-tree versions as well as 2-3 trees and 2-3-4 trees. >

B-trees with relaxed balance

Engineering a Cache-Oblivious Sorting Algorith.

https://findresearcher.sdu.dk:8443/ws/files/179189341/PIIS2211124721000231.pdf

Lipid molecular timeline profiling reveals diurnal crosstalk between the liver and circulation

Two new adaptive sorting algorithms are introduced which perform an optimal number of comparisons with respect to the number of inversions in the input. The first algorithm is based on a new linear time reduction to (non-adaptive) sorting. The second algorithm is based on a new division protocol for the GenericSort algorithm by Estivill-Castro and Wood. From both algorithms we derive I/O-optimal cache-aware and cache-oblivious adaptive sorting algorithms. These are the first I/O-optimal adaptive sorting algorithms.

/pdf/cache-aware-and-cache-oblivious-adaptive-sorting-4ye51biyde.pdf

Rolf Fagerberg

Papers

New and Improved Spanning Ratios for Yao Graphs

B-trees with relaxed balance

Engineering a Cache-Oblivious Sorting Algorith.

Lipid molecular timeline profiling reveals diurnal crosstalk between the liver and circulation

Cache-aware and cache-oblivious adaptive sorting