LMAP: Lightweight Multigene Analyses in PAML

Abstract

BackgroundUncovering how phenotypic diversity arises and is maintained in nature has long been a major interest of evolutionary biologists. Recent advances in genome sequencing technologies have remarkably increased the efficiency to pinpoint genes involved in the adaptive evolution of phenotypes. Reliability of such findings is most often examined with statistical and computational methods using Maximum Likelihood codon-based models (i.e., site, branch, branch-site and clade models), such as those available in codeml from the Phylogenetic Analysis by Maximum Likelihood (PAML) package. While these models represent a well-defined workflow for documenting adaptive evolution, in practice they can be challenging for researchers having a vast amount of data, as multiple types of relevant codon-based datasets are generated, making the overall process hard and tedious to handle, error-prone and time-consuming.ResultsWe introduce LMAP (Lightweight Multigene Analyses in PAML), a user-friendly command-line and interactive package, designed to handle the codeml workflow, namely: directory organization, execution, results gathering and organization for Likelihood Ratio Test estimations with minimal manual user intervention. LMAP was developed for the workstation multi-core environment and provides a unique advantage for processing one, or more, if not all codeml codon-based models for multiple datasets at a time. Our software, proved efficiency throughout the codeml workflow, including, but not limited, to simultaneously handling more than 20 datasets.ConclusionsWe have developed a simple and versatile LMAP package, with outstanding performance, enabling researchers to analyze multiple different codon-based datasets in a high-throughput fashion. At minimum, two file types are required within a single input directory: one for the multiple sequence alignment and another for the phylogenetic tree. To our knowledge, no other software combines all codeml codon substitution models of adaptive evolution. LMAP has been developed as an open-source package, allowing its integration into more complex open-source bioinformatics pipelines. LMAP package is released under GPLv3 license and is freely available at http://lmapaml.sourceforge.net/.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1204-5) contains supplementary material, which is available to authorized users.

The Egyptian Rousette Genome Reveals Unexpected Features of Bat Antiviral Immunity

“…Analyses were run with multiple starting values of both k (2,2.5,4) and u (0.1,1,2) to provide a check against local optimas. These analyses were automated using LMAP v1.0.0 (Maldonado et al, 2016).…”

The Vertebrate TLR Supergene Family Evolved Dynamically by Gene Gain/Loss and Positive Selection Revealing a Host–Pathogen Arms Race in Birds

“…We employed codon models implemented in PAML [51][52][53] and Datamonkey [54] together with amino acid models in TreeSAAP [55]. CODEML in PAML [51] implements likelihood ratio tests (LRT) for comparisons of sophisticated nested site-specific models calculated as twice the difference of the log likelihood between the two models following Chi square distribution with the degrees of freedom corresponding to the difference in the number of parameters between the nested model, i.e., null model and alternate model (positive selection).…”

EasyCodeML: A visual tool for analysis of selection using CodeML

“… a Only a few codon‐based models available. b Maldonado et al, , https://doi.org/10.1186/s12859-016-1204-5. c Schott et al, 2016, http://dx.doi.org/10.1101/059881. …”