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PLL specifications

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Unique identifier OMICS_13196
Name PLL
Alternative name Phylogenetic Likelihood Library
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.2
Stability Stable
Maintained No

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Publication for Phylogenetic Likelihood Library

PLL citations

 (6)
library_books

MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation

2018
BMC Evol Biol
PMCID: 5796505
PMID: 29390973
DOI: 10.1186/s12862-018-1131-3

[…] 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 […]

library_books

Using MOEA with Redistribution and Consensus Branches to Infer Phylogenies

2017
Int J Mol Sci
PMCID: 5796012
PMID: 29278391
DOI: 10.3390/ijms19010062

[…] 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). […]

library_books

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

2016
Syst Biol
PMCID: 5066062
PMID: 27121966
DOI: 10.1093/sysbio/syw037

[…] 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 […]

library_books

Does the choice of nucleotide substitution models matter topologically?

2016
BMC Bioinformatics
PMCID: 4806516
PMID: 27009141
DOI: 10.1186/s12859-016-0985-x

[…] 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 […]

library_books

Clustering Genes of Common Evolutionary History

2016
Mol Biol Evol
PMCID: 4868114
PMID: 26893301
DOI: 10.1093/molbev/msw038

[…] 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 () […]

library_books

An Efficient Independence Sampler for Updating Branches in Bayesian Markov chain Monte Carlo Sampling of Phylogenetic Trees

2015
Syst Biol
PMCID: 4678251
PMID: 26231183
DOI: 10.1093/sysbio/syv051

[…] (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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PLL institution(s)
Heidelberg Institute for Theoretical Studies, Heidelberg Institute, Heidelberg, Germany; Center for Integrative Bioinformatics, Max Ferdinand Perutz Laboratories, University of Vienna, Vienna, Austria; Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria; Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany
PLL funding source(s)
This work was supported by DFG projects STA/860-4, STA/860-3 and STA/860-2, the University of Vienna (Initiativkolleg I059-N), the Austrian Science Fund–FWF (I760B17).

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