Sentence examples for been implemented in phylogenetic from inspiring English sources

Several models specifically developed for RNA sequences have been implemented in phylogenetic packages [e.g. PHASE (Gowri-Shankar and Rattray, 2007) or RAxML (Stamatakis, 2006)], but these models are not widely known.

It has been implemented in most maximum-likelihood and Bayesian phylogenetic software, and is now widely used for routine phylogenetic inference.

Availability: Our algorithms have been implemented in N otung, a freely available phylogenetic reconciliation software package, available at http://www.cs.cmu.edu/~durand/Notung.cmu.edu/~durand/Notung

The cF mixture model has been implemented in QmmRAxML, based on the source code of the phylogenetic inference package RAxML.

Some of the most commonly used methods are those that are implemented in the Phylogenetic Analysis by Maximum Likelihood (PAML) software package [ 29], particularly the codon-based analyses of the program codeml.

The merging procedure is implemented in the TreeBeST phylogenetic engine.

These results were implemented in the following phylogenetic analyses.

The Test for Serial Independence was implemented in the program Phylogenetic Independence v. 2.0 [ 44, 45] with 1000 randomizations.

This method is remarkably fast, does not require any model assumption and is implemented in several popular phylogenetic programs (e.g. MacClade, Maddison and Maddison, 2003).

Its enduring popularity is part historical contingency and part practical: many of the superior methods are more recent and have not yet become widely adopted, and partitioning is implemented in many popular phylogenetic inference programs.

These algorithms can be implemented in software for phylogenetic analysis that involves serial sampling scheme or limited prior knowledge about ancestors of particular clades for calculating tree prior distributions.