scholarly journals RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference

2018 ◽  
Author(s):  
Alexey M. Kozlov ◽  
Diego Darriba ◽  
Tomáš Flouri ◽  
Benoit Morel ◽  
Alexandros Stamatakis
Keyword(s):  
Search Algorithm ◽  
Phylogenetic Inference ◽  
Biological Research ◽  
Bootstrap Support ◽  
Link Type ◽  
Optimal Tree ◽  
Tree Space ◽  
User Friendly ◽  
Tree Search Algorithm ◽  
Improved Accuracy

AbstractMotivationPhylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture, and medicine. Finding the optimal tree under the popular maximum like-lihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets.ResultsWe present RAxML-NG, a from scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML- NG offers improved accuracy, flexibility, speed, scalability, and usability compared to RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and a the recently introduced transfer bootstrap support metric.AvailabilityThe code is available under GNU GPL at https://github.com/amkozlov/raxml-ng.RAxML-NG web service (maintained by Vital- IT) is available at https://raxml-ng.vital-it.ch/[email protected]

scholarly journals RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

2019 ◽  
Vol 35 (21) ◽  
pp. 4453-4455 ◽  
Author(s):  
Alexey M Kozlov ◽  
Diego Darriba ◽  
Tomáš Flouri ◽  
Benoit Morel ◽  
Alexandros Stamatakis
Keyword(s):  
Maximum Likelihood ◽  
Search Algorithm ◽  
Phylogenetic Inference ◽  
Supplementary Information ◽  
Biological Research ◽  
Bootstrap Support ◽  
Optimal Tree ◽  
User Friendly ◽  
Tree Search Algorithm ◽  
Improved Accuracy

Abstract Motivation Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets. Results We present RAxML-NG, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML-NG offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and the recently introduced transfer bootstrap support metric. Availability and implementation The code is available under GNU GPL at https://github.com/amkozlov/raxml-ng. RAxML-NG web service (maintained by Vital-IT) is available at https://raxml-ng.vital-it.ch/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era

2019 ◽  
Author(s):  
Bui Quang Minh ◽  
Heiko Schmidt ◽  
Olga Chernomor ◽  
Dominik Schrempf ◽  
Michael Woodhams ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Software Package ◽  
Genomic Data ◽  
Phylogenetic Inference ◽  
Sequence Evolution ◽  
Computational Approaches ◽  
Link Type ◽  
New Models ◽  
User Friendly

AbstractIQ-TREE (http://www.iqtree.org) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.

Pedigree and Pedigree Import Wizard

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 552g-553
Author(s):  
Shahrokh Khandizadeh
Keyword(s):  
Additional Data ◽  
File Format ◽  
Fruit Crops ◽  
Operating Environment ◽  
Agronomic Characteristics ◽  
Link Type ◽  
Plant Characteristics ◽  
User Friendly

Pedigree for Windows is a user-friendly program that allows the user to trace agronomic characteristics, draw pedigrees, and view images of several fruit crops, including more than 1400 apple, 800 strawberry, 800 almond, 100 blackberry, 80 blueberry, 790 pear, 200 raspberry examples. Pedigree Import Wizard®© for Windows is an add-on software for users who are interested in importing their research or breeding data records of fruit, flower, and plant characteristics and any related images into Pedigree for Windows. Pedigree for Windows and Pedigree Import Wizard have been designed so that a user familiar with the Windows operating environment should have little need to refer to the documentation provided with the program. Pedigree Import Wizard uses a comma-separated value (csv) file format under the MS Excel environment. This option allows the user to add or import additional data to the existing database that are already stored in other software such as Lotus, Excel, Access, QuattroPro, WordPerfect, and MS Word tables, etc., as long as they work under the Windows environment. A free demo version of Pedigree and Pedigree Import Wizard for Windows is available from http://www.pgris.com.

scholarly journals Incorporation of Potential Fields and Motion Primitives for the Collision Avoidance of Unmanned Aircraft

2021 ◽  
Vol 11 (7) ◽  
pp. 3103
Author(s):  
Kyuman Lee ◽  
Daegyun Choi ◽  
Donghoon Kim
Keyword(s):  
Collision Avoidance ◽  
Search Algorithm ◽  
Unmanned Aircraft ◽  
Artificial Potential Field ◽  
Tree Search ◽  
Local Minima ◽  
Collision Risk ◽  
Motion Primitives ◽  
Multiple Uavs ◽  
Tree Search Algorithm

Collision avoidance (CA) using the artificial potential field (APF) usually faces several known issues such as local minima and dynamically infeasible problems, so unmanned aerial vehicles’ (UAVs) paths planned based on the APF are safe only in a certain environment. This research proposes a CA approach that combines the APF and motion primitives (MPs) to tackle the known problems associated with the APF. Since MPs solve for a locally optimal trajectory with respect to allocated time, the trajectory obtained by the MPs is verified as dynamically feasible. When a collision checker based on the k-d tree search algorithm detects collision risk on extracted sample points from the planned trajectory, generating re-planned path candidates to avoid obstacles is performed. After rejecting unsafe route candidates, one applies the APF to select the best route among the remaining safe-path candidates. To validate the proposed approach, we simulated two meaningful scenario cases—the presence of static obstacles situation with local minima and dynamic environments with multiple UAVs present. The simulation results show that the proposed approach provides smooth, efficient, and dynamically feasible pathing compared to the APF.

scholarly journals Enhanced Reinforcement Learning Method Combining One-Hot Encoding-Based Vectors for CNN-Based Alternative High-Level Decisions

2021 ◽  
Vol 11 (3) ◽  
pp. 1291
Author(s):  
Bonwoo Gu ◽  
Yunsick Sung
Keyword(s):  
Reinforcement Learning ◽  
Search Algorithm ◽  
Classification Criteria ◽  
Tree Search ◽  
Learning Method ◽  
Board Game ◽  
Ancient China ◽  
Monte Carlo Tree Search ◽  
High Level ◽  
Tree Search Algorithm

Gomoku is a two-player board game that originated in ancient China. There are various cases of developing Gomoku using artificial intelligence, such as a genetic algorithm and a tree search algorithm. Alpha-Gomoku, Gomoku AI built with Alpha-Go’s algorithm, defines all possible situations in the Gomoku board using Monte-Carlo tree search (MCTS), and minimizes the probability of learning other correct answers in the duplicated Gomoku board situation. However, in the tree search algorithm, the accuracy drops, because the classification criteria are manually set. In this paper, we propose an improved reinforcement learning-based high-level decision approach using convolutional neural networks (CNN). The proposed algorithm expresses each state as One-Hot Encoding based vectors and determines the state of the Gomoku board by combining the similar state of One-Hot Encoding based vectors. Thus, in a case where a stone that is determined by CNN has already been placed or cannot be placed, we suggest a method for selecting an alternative. We verify the proposed method of Gomoku AI in GuPyEngine, a Python-based 3D simulation platform.

scholarly journals Gesture commands for controlling high-level UAV behavior

2021 ◽  
Vol 3 (6) ◽  
Author(s):  
John Akagi ◽  
T. Devon Morris ◽  
Brady Moon ◽  
Xingguang Chen ◽  
Cameron K. Peterson
Keyword(s):  
Search Algorithm ◽  
Dynamic Environment ◽  
List Type ◽  
Hardware In The Loop ◽  
Monte Carlo Tree Search ◽  
Natural Interface ◽  
Constrained Environments ◽  
Novel Variant ◽  
High Level ◽  
Tree Search Algorithm

Abstract Directing groups of unmanned air vehicles (UAVs) is a task that typically requires the full attention of several operators. This can be prohibitive in situations where an operator must pay attention to their surroundings. In this paper we present a gesture device that assists operators in commanding UAVs in focus-constrained environments. The operator influences the UAVs’ behavior by using intuitive hand gesture movements. Gestures are captured using an accelerometer and gyroscope and then classified using a logistic regression model. Ten gestures were chosen to provide behaviors for a group of fixed-wing UAVs. These behaviors specified various searching, following, and tracking patterns that could be used in a dynamic environment. A novel variant of the Monte Carlo Tree Search algorithm was developed to autonomously plan the paths of the cooperating UAVs. These autonomy algorithms were executed when their corresponding gesture was recognized by the gesture device. The gesture device was trained to classify the ten gestures and accurately identified them 95% of the time. Each of the behaviors associated with the gestures was tested in hardware-in-the-loop simulations and the ability to dynamically switch between them was demonstrated. The results show that the system can be used as a natural interface to assist an operator in directing a fleet of UAVs. Article highlights A gesture device was created that enables operators to command a group of UAVs in focus-constrained environments. Each gesture triggers high-level commands that direct a UAV group to execute complex behaviors. Software simulations and hardware-in-the-loop testing shows the device is effective in directing UAV groups.

scholarly journals CASA: An Efficient Automated Assignment of Protein Mainchain NMR Data Using an Ordered Tree Search Algorithm

2005 ◽  
Vol 33 (4) ◽  
pp. 261-279 ◽  
Author(s):  
Jianyong Wang ◽  
Tianzhi Wang ◽  
Erik R. P. Zuiderweg ◽  
Gordon M. Crippen
Keyword(s):  
Search Algorithm ◽  
Automated Assignment ◽  
Tree Search ◽  
Nmr Data ◽  
Ordered Tree ◽  
Tree Search Algorithm
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