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LMAP: Lightweight Multigene Analyses in PAML.

Emanuel Maldonado1, Daniela Almeida1,2, Tibisay Escalona1,2

  • 1CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.

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Summary

Researchers can now streamline adaptive evolution analyses with LMAP (Lightweight Multigene Analyses in PAML), a new software package. LMAP automates complex workflows for multiple gene datasets, saving time and reducing errors in evolutionary biology research.

Keywords:
Adaptive evolutionCodon substitution modelsMulti-coreMultigenePAMLSoftware packagecodeml

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Area of Science:

  • Evolutionary Biology
  • Genomics
  • Bioinformatics

Background:

  • Phenotypic diversity is a key area of evolutionary biology.
  • Genome sequencing advances aid in identifying genes related to adaptive evolution.
  • Maximum Likelihood codon-based models in PAML are standard for analyzing adaptive evolution but are complex for large datasets.

Purpose of the Study:

  • To develop a user-friendly software package to simplify the analysis of adaptive evolution using PAML.
  • To automate and streamline the codeml workflow for researchers handling large datasets.
  • To improve the efficiency and reduce errors in analyzing multiple gene datasets.

Main Methods:

  • Introduction of LMAP (Lightweight Multigene Analyses in PAML), a command-line and interactive package.
  • LMAP automates directory organization, codeml execution, and results gathering for Likelihood Ratio Test estimations.
  • The software is designed for multi-core workstations to process multiple datasets and codeml models concurrently.

Main Results:

  • LMAP efficiently handles the entire codeml workflow with minimal user intervention.
  • The package can simultaneously process over 20 datasets.
  • Demonstrated efficiency in managing complex analyses involving multiple codon-based models.

Conclusions:

  • LMAP is a versatile, high-performance package for high-throughput analysis of codon-based datasets.
  • Requires only multiple sequence alignment and phylogenetic tree files for input.
  • LMAP integrates all codeml codon substitution models for adaptive evolution analysis and is open-source.