IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) 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.

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

10.1101/849372 ◽

2019 ◽

Cited By ~ 8

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.

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cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large whole genome sequencing datasets

10.1101/2020.10.15.340901 ◽

2020 ◽

Author(s):

Ryan D. Crawford ◽

Evan S. Snitkin

Keyword(s):

Phylogenetic Analysis ◽

Genome Sequencing ◽

Software Package ◽

Genomic Data ◽

Phylogenetic Inference ◽

R Package ◽

Core Gene ◽

Whole Genome ◽

Rapid Generation ◽

User Friendly

AbstractThe quantity of genomic data is expanding at an increasing rate. Tools for phylogenetic analysis which scale to the quantity of available data are required. We present cognac, a user-friendly software package to rapidly generate concatenated gene alignments for phylogenetic analysis. We applied this tool to generate core gene alignments for very large genomic datasets, including a dataset of over 11,000 genomes from the genus Escherichia containing 1,353 genes, which was constructed in less than 17 hours. We have released cognac as an R package (https://github.com/rdcrawford/cognac) with customizable parameters for adaptation to diverse applications.

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

Bioinformatics ◽

10.1093/bioinformatics/btz305 ◽

2019 ◽

Vol 35 (21) ◽

pp. 4453-4455 ◽

Cited By ~ 286

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.

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cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets

BMC Bioinformatics ◽

10.1186/s12859-021-03981-4 ◽

2021 ◽

Vol 22 (1) ◽

Cited By ~ 1

Author(s):

Ryan D. Crawford ◽

Evan S. Snitkin

Keyword(s):

Phylogenetic Analysis ◽

Software Package ◽

Phylogenetic Inference ◽

R Package ◽

Core Gene ◽

Data Driven ◽

Marker Genes ◽

Data Driven Approach ◽

Rapid Generation ◽

User Friendly

Abstract Background The quantity of genomic data is expanding at an increasing rate. Tools for phylogenetic analysis which scale to the quantity of available data are required. To address this need, we present cognac, a user-friendly software package to rapidly generate concatenated gene alignments for phylogenetic analysis. Results We illustrate that cognac is able to rapidly identify phylogenetic marker genes using a data driven approach and efficiently generate concatenated gene alignments for very large genomic datasets. To benchmark our tool, we generated core gene alignments for eight unique genera of bacteria, including a dataset of over 11,000 genomes from the genus Escherichia producing an alignment with 1353 genes, which was constructed in less than 17 h. Conclusions We demonstrate that cognac presents an efficient method for generating concatenated gene alignments for phylogenetic analysis. We have released cognac as an R package (https://github.com/rdcrawford/cognac) with customizable parameters for adaptation to diverse applications.

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An efficient coalescent epoch model for Bayesian phylogenetic inference

10.1101/2021.06.28.450225 ◽

2021 ◽

Author(s):

Remco Bouckaert

Keyword(s):

Monte Carlo ◽

Population Size ◽

Graphical User Interface ◽

Genomic Data ◽

Phylogenetic Inference ◽

Population Sizes ◽

Calibrated Simulation ◽

User Friendly ◽

Bayesian Phylogenetic Inference ◽

Friendly Graphical User Interface

We present a two headed approach called Bayesian Integrated Coalescent Epoch PlotS (BICEPS) for efficient inference of coalescent epoch models. Firstly, we integrate out population size parameters and secondly we introduce a set of more powerful Markov chain Monte Carlo (MCMC) proposals for flexing and stretching trees. Even though population sizes are integrated out and not explicitly sampled through MCMC, we are still able to generate samples from the population size posteriors, which allows demographic reconstruction through time. Altogether, BICEPS can be considered a more muscular version of the popular Bayesian skyline model. We demonstrate its power and correctness by a well calibrated simulation study. Furthermore, we demonstrate with an application to COVID-19 genomic data that some analyses that have trouble converging with the traditional Bayesian skyline prior and standard MCMC proposals can do well with the BICEPS approach. BICEPS is available as open source package for BEAST 2 under GPL license and has a user friendly graphical user interface.

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Computation and statistical comparison of the parameter estimates of the Michaelis-Menten model using nonlinear optimization. ENZ 2.0, a user-friendly software package

Computer Methods and Programs in Biomedicine ◽

10.1016/0169-2607(92)90096-p ◽

1992 ◽

Vol 37 (2) ◽

pp. 149-150 ◽

Cited By ~ 1

Author(s):

Hedwig K. Stals ◽

Peter E. Declercq

Keyword(s):

Nonlinear Optimization ◽

Software Package ◽

Parameter Estimates ◽

Statistical Comparison ◽

User Friendly

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Recent and Planned Developments of the Program OxCal

Radiocarbon ◽

10.1017/s0033822200057878 ◽

2013 ◽

Vol 55 (2) ◽

pp. 720-730 ◽

Cited By ~ 641

Author(s):

Christopher Bronk Ramsey ◽

Sharen Lee

Keyword(s):

Statistical Analysis ◽

Statistical Methods ◽

Software Package ◽

Model Averaging ◽

Data Sets ◽

Radiocarbon Dates ◽

New Approach ◽

New Models ◽

Multiphase Models ◽

Deposition Models

OxCal is a widely used software package for the calibration of radiocarbon dates and the statistical analysis of 14C and other chronological information. The program aims to make statistical methods easily available to researchers and students working in a range of different disciplines. This paper will look at the recent and planned developments of the package. The recent additions to the statistical methods are primarily aimed at providing more robust models, in particular through model averaging for deposition models and through different multiphase models. The paper will look at how these new models have been implemented and explore the implications for researchers who might benefit from their use. In addition, a new approach to the evaluation of marine reservoir offsets will be presented. As the quantity and complexity of chronological data increase, it is also important to have efficient methods for the visualization of such extensive data sets and methods for the presentation of spatial and geographical data embedded within planned future versions of OxCal will also be discussed.

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A user-friendly general-purpose predictive software package for food safety

Journal of Food Engineering ◽

10.1016/j.jfoodeng.2010.11.021 ◽

2011 ◽

Vol 104 (2) ◽

pp. 173-185 ◽

Cited By ~ 19

Author(s):

Amit Halder ◽

Ashish Dhall ◽

Ashim K. Datta ◽

D. Glenn Black ◽

P.M. Davidson ◽

...

Keyword(s):

Food Safety ◽

Software Package ◽

General Purpose ◽

User Friendly ◽

Predictive Software

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A General-Purpose Software for Menu Design of CAD Projects

13th Computers in Engineering Conference ◽

10.1115/cie1993-0074 ◽

1993 ◽

Author(s):

Y. C. Pao

Keyword(s):

Software Package ◽

Computer Programs ◽

General Purpose ◽

Final Report ◽

Sample Design ◽

Main Menu ◽

Sample Application ◽

User Friendly ◽

Four Bar Linkage ◽

General Purpose Software

Abstract A software package MenuCAD has been developed for the general need of designing menu-driven, user-friendly CAD computer programs. The main menu is formatted similar to the major contents in the final report of the design project including Contents, Analysis, Sample Design Cases, Illustrations and Tables, References, and Program Listings. Sub-menus are further divided into items delineating the steps involved in the design. Screen help messages are provided for design of the main menu and sub-menus interactively and for applying the arrow keys on the keyboard to select a sub-menus and a particular item in the sub-menu in order to execute a desired design step. MenuCAD builds the framework, its user has to supplement with a subroutine ExecItem for describing the special features and for directing how each design step should be executed in the project. A CAD design of four-bar linkage project is presented as a sample application of this package.

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