How do you cite PhyML?

How do you cite PhyML?

PhyML 3.0: new algorithms, methods and utilities If you use SMS, please cite: “SMS: Smart Model Selection in PhyML.”

What is PhyML?

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology. It implements new algorithms to search the space of tree topologies with user-defined intensity.

How do you use PhyML in geneious?

Install the plugin by downloading the gplugin file and dragging it in to Geneious Prime or use the plugin manager in Geneious Prime (under Tools – Plugins in the menu). Once installed, run the plugin by selecting a multiple sequence alignment and clicking on Tree in the toolbar.

How do you cite RAxML?

New RAxML citation When using RAxML please cite the following paper: A. Stamatakis: “RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies”. In Bioinformatics, 2014, open access.

How long does RAxML take?

3): RAxML was the slowest, taking between 647 and 2150 hours to produce trees, FastTree the fastest, taking between 2 and 6.3 hours, and RAxML-Limited in between, taking between 10 and 50 hours.

What is Phylip format?

PHYLIP format is a plain text format containing exactly two sections: a header describing the dimensions of the alignment, followed by the multiple sequence alignment itself.

How do I run RAxML on Windows?

Just download the zip file from Github ( https://github.com/stamatak/standard-RAxML ) and unpack it. Then open a command prompt window, go to the \standard-RAxML-master\WindowsExecutables_v8. 2.4 directory, and execute the program.

What is RAxML Ng?

RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.

What does RAxML do?

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for post- analyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads.

How do you cite a PHYLIP?

PHYLIP

1. Description. a free package of software programs for inferring phylogenies.
2. Installation. Use the following command to install this title with the CLI client: $ sbgrid-cli install phylip.
3. Primary Citation* J. Felsenstein. 1989.
4. Citation Note. PHYLIP may also be cited as follows: “Felsenstein, J. 2005.

How do you run a PHYLIP?

To start a PHYLIP program in DOS or UNIX enter the name program you wish to run. In Windows or Macintosh (double) click on the program. You must quit before starting a new analysis. In PHYLIP, enter ‘I’ (to change to sequential), change any other options, and then ‘y’ to begin the analysis.

What is PHYLIP format?

Why is PhyML so widely used?

Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology. Since the original publication ( Guindon and Gascuel 2003 ), PhyML has been widely used (>1,250 citations in ISI Web of Science), due to its simplicity and a fair accuracy/speed compromise.

How do I use the PhyML interface?

The default is to use the PHYLIP-like text interface (Figure1) by simply typing ‘phyml’in a command-line window or by clicking on the PhyML icon (seeSection4.3). Afterentering the name of the input sequence file, a list of sub-menus helps the users to set upthe analysis. There are currently four distinct sub-menus:

What are the results files of PhyML?

PhyML produces several results files: _phyml_lk.txt : site likelihood value(s) _phyml_tree.txt : inferred tree(s) _phyml_stat.txt : detailed execution statistics _phyml_boot_trees.txt : bootstrap trees (special case)

What is the difference between PhyML and phytime?

It implements a large number of substitution models coupled to efficient options to search the space of phylogenetic tree topologies. PhyTime is another tool in the PhyML package that focuses on divergence date estimation in a Bayesian setting.