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|Alternative name||Phylogenetic Likelihood Library|
|Interface||Command line interface|
|Restrictions to use||None|
|Operating system||Unix/Linux, Mac OS, Windows|
|License||GNU General Public License version 3.0|
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Publication for Phylogenetic Likelihood Library
MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation
[…] MPBoot uses the phylogenetic likelihood library (PLL)  for efficient parsimony computations. To reduce the computational cost of SPR searches, the PLL employs a radius that restricts the maximum number of nodes bet […]
Using MOEA with Redistribution and Consensus Branches to Infer Phylogenies
[…] ttings of these software packages are default. Because the evaluation method is diverse in different software, we reevaluated the optimal trees generated by all algorithm and software using Bio++ and Phylogenetic Likelihood Library (PPL). In , we can find MOEA-RC is much better than the other software in terms of likelihood. However, for parsimony, it is only better for one dataset (rbcl_55). […]
Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices
[…] hat one should run each program as often as possible to ensure more reliable results and one should also use different programs.As a further step, we plan to implement the PTA data structure into the phylogenetic likelihood library () and to perform the analysis also with SPR. Here, careful considerations are necessary to achieve a high parallel efficiency ().While the PTA helps to speed up tree s […]
Does the choice of nucleotide substitution models matter topologically?
[…] ria is jModelTest 2 . However, jModelTest relies on PHYML  to calculate likelihood scores for a given substitution model and tree. PHYML is relatively slow compared to RaxML (v. 8.1.7 ) and the Phylogenetic Likelihood Library (PLL ) that relies on the same phylogenetic likelihood kernel implementation as RaxML. For instance, optimizing the model parameters and branch lengths on a fixed tre […]
Clustering Genes of Common Evolutionary History
[…] ch is statistically robust () and enables us to use a likelihood criterion for cluster membership comparisons and cluster number decisions. For each locus, we infer the ML phylogenetic tree using the Phylogenetic Likelihood Library (PLL) ().In the experiments described in this article, we use PLL’s full ML estimation with tree search. We use either the General Time Reversible model (GTR) model () […]
An Efficient Independence Sampler for Updating Branches in Bayesian Markov chain Monte Carlo Sampling of Phylogenetic Trees
[…] (see ). For 11.1% of all branches, the NR method did not converge to the optimum. This exclusively affects CPDs with a cv close to 1 (i.e., exponential distributions) and a mode at or close to 0. The phylogenetic likelihood library (PLL) () that is used for likelihood evaluations in ExaBayes does not allow for evaluation of values below a certain threshold for reasons of numerical stability. The t […]
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