Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a completely new tree display engine, together with numerous new features. For example, a new dataset type has been added (MEME motifs), while annotation options have been expanded for several existing ones. Node metadata display options have been extended and now also support non-numerical categorical values, as well as multiple values per node. Direct manual annotation is now available, providing a set of basic drawing and labeling tools, allowing users to draw shapes, labels and other features by hand directly onto the trees. Support for tree and dataset scales has been extended, providing fine control over line and label styles. Unrooted tree displays can now use the equal-daylight algorithm, proving a much greater display clarity. The user account system has been streamlined and expanded with new navigation options and currently handles >1 million trees from >70 000 individual users.

Attitude Adjustment of a Quadruped Robot in the Air

When the moments of climbing robots, jumping robots, and gliding robots extend to the air, they should reorient themselves to minimize the damage during a fall. Based on imitating a falling cat, robot can reorientate about one axis without external force. In this paper, an extended attitude adjustment method for quadruped robots is presented to achieve three degrees of freedom attitude adjustment with the movement of four robotic limbs. A mathematical model of a falling robot is established based on the multi-rigid-body unrooted tree system. The response of the prototype’s azimuth to the input of the cylindrical hinges is analyzed. A 3D model prototype was designed in SolidWorks and simulation experiments were carried out in ADAMS. Prototype were manufactured with a 3D printer, to validate the attitude adjustment method. The simulation and experimental results showed that the main body of the prototype was able to rotate respectively 89 degrees in the X-axis, 89 degrees in Y-axis, and 49 degrees in Z-axis in a movement cycle of the robotic limbs.

An optimal algorithm for computing all subtree repeats in trees

Given a labelled tree T , our goal is to group repeating subtrees of T into equivalence classes with respect to their topologies and the node labels. We present an explicit, simple and time-optimal algorithm for solving this problem for unrooted unordered labelled trees and show that the running time of our method is linear with respect to the size of T . By unordered, we mean that the order of the adjacent nodes (children/neighbours) of any node of T is irrelevant. An unrooted tree T does not have a node that is designated as root and can also be referred to as an undirected tree. We show how the presented algorithm can easily be modified to operate on trees that do not satisfy some or any of the aforementioned assumptions on the tree structure; for instance, how it can be applied to rooted, ordered or unlabelled trees.

Phylogenetic analysis among Indian squill Urginea indica Kunth. Liliaceae

In the present study on Urginea indica, twelve different populations from southern part of India is considered. Fifteen parameters have been scored for each population to understand the relationship between different races. The main objective is to trace phylogeny in populations of U. indica to construct phylogenetic tree. The phylogenetic tree obtained is an unrooted tree. The parsimony tree describes that Shimoga and Chamundi hill populations have parallely evolved and forms the out group. Dopaegowdanapura population has given rise to Gopalaswamy betta, Gopalaswamy betta has given rise to Banganavadi and Banganavadi has given rise to one population which is missing in the tree and the missing population has given rise to Gorur on one hand and to Krishna Raja Sagar island and Gandhi Krishi Vighnayana Kendra on the other hand. Krishna Raja Sagar island and Gandhi Krishi Vighnayana Kendra shares a common clade. Gorur has given rise to Papanasini and Papanasini has given rise to Channamallipura, from Channamallipura another population has been evolved which is missing and the missing population has given rise to Basavanahalli and Ranganthittu which shares a Common clade. The Parsimony tree shows that these populations have evolved parallel. Dopaegowdanapura is the oldest from which all others are evolved. Ranganathittu and Basavanahalli form the youngest and latest. Therefore it is an unrooted tree with distance. Each population varied in their morphology and chromosome number and called as cytotypes. Difference in morphological character is mainly because of genetic characters. Habitat does not seem to play major role to mould morphological features.

Characterisation of Genetic Diversity in ICARDA Core Collection of Cultivated Barley (Hordeum vulgare L.)

Out of the total accessions of cultivated barley, held at ICARDA, a subset core collection consisting of 153 accessions originating from different countries was established. Genetic diversity of the core collection was studied using AFLP markers. The accessions were grouped into different geographic sub-regions and the total genetic variation was estimated using Popgene software. Genetic distance matrix was computed and hierarchical unrooted tree was performed using Phylip software package. Our results demonstrate that the AFLP markers were highly informative and were useful in generating a meaningful classification of the cultivated barley that we determined as a subset of core collection.    

Unrooted trees for numerical taxonomy

It is common to represent taxonomic hierarchies of related objects (such as similar plant or animal species or languages of the same family) by rooted trees with labelled terminal vertices which represent the objects. The multivariate data comparing numerous characteristics of the objects is first reduced to indices of similarity (or more often of dissimilarity) between each pair of objects. These are used to classify the objects into groups which are then depicted on a tree. This paper shows that an unrooted tree with labelled terminal vertices may provide a better representation of the relationships between the objects because the similarity indices are required to conform to fewer restrictions. Also for a given number of terminal vertices, there are fewer unrooted than rooted trees so that studies using probability distributions of trees or seeking the most suitable tree to represent the data are more practicable.

Unrooted trees for numerical taxonomy

It is common to represent taxonomic hierarchies of related objects (such as similar plant or animal species or languages of the same family) by rooted trees with labelled terminal vertices which represent the objects. The multivariate data comparing numerous characteristics of the objects is first reduced to indices of similarity (or more often of dissimilarity) between each pair of objects. These are used to classify the objects into groups which are then depicted on a tree.This paper shows that an unrooted tree with labelled terminal vertices may provide a better representation of the relationships between the objects because the similarity indices are required to conform to fewer restrictions. Also for a given number of terminal vertices, there are fewer unrooted than rooted trees so that studies using probability distributions of trees or seeking the most suitable tree to represent the data are more practicable.