scholarly journals siMBa—a simple graphical user interface for the Bayesian phylogenetic inference program MrBayes

2014 ◽  
Vol 13 (4) ◽  
Author(s):  
Bagdevi Mishra ◽  
Marco Thines
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Phylogenetic Inference ◽  
Bayesian Phylogenetic Inference

scholarly journals raxmlGUI 2.0: a graphical interface and toolkit for phylogenetic analyses using RAxML

2019 ◽  
Author(s):  
Daniel Edler ◽  
Johannes Klein ◽  
Alexandre Antonelli ◽  
Daniele Silvestro
Keyword(s):  
User Interface ◽  
Maximum Likelihood ◽  
Operating Systems ◽  
Graphical User Interface ◽  
Phylogenetic Analyses ◽  
Phylogenetic Inference ◽  
Graphical Interface ◽  
Front End ◽  
Set Up ◽  
Intuitive Interface

AbstractRaxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. Here we present raxmlGUI 2.0, a complete rewrite of the GUI which seamlessly integrates RAxML binaries for all major operating systems with an intuitive graphical front-end to set up and run phylogenetic analyses. Our program offers automated pipelines for analyses that require multiple successive calls of RAxML and built-in functions to concatenate alignment files while automatically specifying the appropriate partition settings. In addition to RAxML 8.x, raxmlGUI 2.0 also supports the new RAxML Next Generation. RaxmlGUI facilitates phylogenetic analyses by coupling an intuitive interface with the unmatched performance of RAxML.

scholarly journals An efficient coalescent epoch model for Bayesian phylogenetic inference

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.

HOW TO USE CROP GROWTH MODEL WOFOST FOR FORECASTING GROWTH AND YIELD OF A CROP

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
LAL SINGH ◽  
PARMEET SINGH ◽  
RAIHANA HABIB KANTH ◽  
PURUSHOTAM SINGH ◽  
SABIA AKHTER ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Input Data ◽  
Growth And Yield ◽  
Weather Data ◽  
Data Sets ◽  
Crop Growth Model ◽  
Control Center ◽  
Field Crops ◽  
Crop Calendar

WOFOST version 7.1.3 is a computer model that simulates the growth and production of annual field crops. All the run options are operational through a graphical user interface named WOFOST Control Center version 1.8 (WCC). WCC facilitates selecting the production level, and input data sets on crop, soil, weather, crop calendar, hydrological field conditions, soil fertility parameters and the output options. The files with crop, soil and weather data are explained, as well as the run files and the output files. A general overview is given of the development and the applications of the model. Its underlying concepts are discussed briefly.

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