dependencies.bib

@article{Nakamura2018,
author = {Nakamura, Tsukasa and Yamada, Kazunori D and Tomii, Kentaro and Katoh, Kazutaka},
doi = {10.1093/bioinformatics/bty121},
editor = {Hancock, John},
issn = {1367-4803},
journal = {Bioinformatics},
mendeley-groups = {AlanPaper},
month = {jul},
number = {14},
pages = {2490--2492},
publisher = {Oxford University Press},
title = {{Parallelization of MAFFT for large-scale multiple sequence alignments}},
volume = {34},
year = {2018}
}

@article{Capella-Gutierrez2009,
author = {Capella-Gutierrez, S. and Silla-Martinez, J. M. and Gabaldon, T.},
doi = {10.1093/bioinformatics/btp348},
issn = {1367-4803},
journal = {Bioinformatics},
month = {aug},
number = {15},
pages = {1972--1973},
title = {{trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses}},
url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btp348},
volume = {25},
year = {2009}
}

@article{Simao2015,
author = {Sim{\~{a}}o, Felipe A. and Waterhouse, Robert M. and Ioannidis, Panagiotis and Kriventseva, Evgenia V. and Zdobnov, Evgeny M.},
doi = {10.1093/bioinformatics/btv351},
issn = {1367-4803},
journal = {Bioinformatics},
month = {oct},
number = {19},
pages = {3210--3212},
title = {{BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs}},
url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv351},
volume = {31},
year = {2015}
}

@article{Minh2020,
abstract = {IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.},
author = {Minh, Bui Quang and Schmidt, Heiko A and Chernomor, Olga and Schrempf, Dominik and Woodhams, Michael D and von Haeseler, Arndt and Lanfear, Robert},
doi = {10.1093/molbev/msaa015},
editor = {Teeling, Emma},
issn = {0737-4038},
journal = {Molecular Biology and Evolution},
month = {may},
number = {5},
pages = {1530--1534},
title = {{IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era}},
url = {https://academic.oup.com/mbe/article/37/5/1530/5721363},
volume = {37},
year = {2020}
}

@article{Barbera2019,
author = {Barbera, Pierre and Kozlov, Alexey M and Czech, Lucas and Morel, Benoit and Darriba, Diego and Flouri, Tom{\'{a}}{\v{s}} and Stamatakis, Alexandros},
doi = {10.1093/sysbio/syy054},
editor = {Posada, David},
issn = {1063-5157},
journal = {Systematic Biology},
month = {mar},
number = {2},
pages = {365--369},
title = {{EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences}},
url = {https://academic.oup.com/sysbio/article/68/2/365/5079844},
volume = {68},
year = {2019}
}