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FranziskaReden edited this page Aug 28, 2023 · 1 revision

EvoNAPS

Introduction

The EvoNAPS database provides a large variety of phylogenetic trees as well as empirical parameter estimates of a diverse set of sequence evolution (SE) models. The main purpose of the database is to provide meaningful input for sequence simulations as phylogenetic studies have come to heavily rely on simulated data. The database offers various filter options to enable the user to find alignments, SE models or trees that fit their requirements.

The parameter estimates stored in EvoNAPS were gathered using the phylogenetic inference software IQ-Tree (v.2.2.0.5) (Minh, 2022) and are based on biological alignments. The alignments were gathered from existing published sources, namely the online respiratory provided by Rob Lanfear (Lanfear, 2019) as well as the PANDIT (Whelan, 2006) and the OrthoMaM (Douzery, 2014) databases.

So-far, the EvoNAPS database holds:

  • around 22,600 DNA alignments
  • around 6,600 protein alignments and
  • over 64,000 phylogenetic trees.

Overview

This repository includes scripts regarding the MySQL database itself (such as the create statements and example import commands):

Additionally, all scripts used to create the data in the EvoNAPS database can be found here:

References

Douzery, E. J. P., Scornavacca, C., Romiguier, J., Belkhir, K., Galtier, N., Delsuc, F., & Ranwez, V. (2014). OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals. Molecular Biology and Evolution, 31(7), 1923-1928. https://doi.org/10.1093/molbev/msu132

Lanfear, R. (2019). BenchmarkAlignments. https://github.com/roblanf/BenchmarkAlignments/

Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020). IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol Biol Evol, 37(5), 1530-1534. https://doi.org/10.1093/molbev/msaa015

Whelan, S., Bakker, P., Quevillon, E., Rodriguez, N., & Goldman, N. (2006). PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic acids research, 34, D327-331. https://doi.org/10.1093/nar/gkj087

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