@article{10.1093/molbev/mst010,
    author = "Katoh, Kazutaka and Standley, Daron M.",
    title = "{MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability}",
    journal = "Molecular Biology and Evolution",
    volume = "30",
    number = "4",
    pages = "772-780",
    year = "2013",
    month = "01",
    abstract = "{We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.}",
    issn = "0737-4038",
    doi = "10.1093/molbev/mst010",
    url = "https://doi.org/10.1093/molbev/mst010",
    eprint = "https://academic.oup.com/mbe/article-pdf/30/4/772/6420419/mst010.pdf"
}

@article{Emms2019,
    author = "Emms, David M. and Kelly, Steven",
    type = "Journal Article",
    title = "OrthoFinder: phylogenetic orthology inference for comparative genomics",
    journal = "Genome Biology",
    number = "1",
    doi = "10.1186/s13059-019-1832-y",
    volume = "20",
    pages = "238",
    url = "https://doi.org/10.1186/s13059-019-1832-y",
    year = "2019",
    abstract = "Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics. Each output is benchmarked on appropriate real or simulated datasets, and where comparable methods exist, OrthoFinder is equivalent to or outperforms these methods. Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. Finally, OrthoFinder’s comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. OrthoFinder is available at https://github.com/davidemms/OrthoFinder.",
    isbn = "1474-760X",
    DA = "2019/11/14"
}

@article{10.1371/journal.pbio.3001007,
    author = "Steenwyk, Jacob L. and Buida, III, Thomas J. and Li, Yuanning and Shen, Xing-Xing and Rokas, Antonis",
    doi = "10.1371/journal.pbio.3001007",
    journal = "PLOS Biology",
    publisher = "Public Library of Science",
    title = "ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference",
    year = "2020",
    month = "12",
    volume = "18",
    url = "https://doi.org/10.1371/journal.pbio.3001007",
    pages = "1-17",
    abstract = "Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation of substitutions, are thought to negatively impact phylogenetic inference. Thus, several different trimming strategies have been developed for identifying and removing these sites prior to phylogenetic inference. However, a recent study reported that doing so can worsen inference, underscoring the need for alternative alignment trimming strategies. Here, we introduce ClipKIT, an alignment trimming software that, rather than identifying and removing putatively phylogenetically uninformative sites, instead aims to identify and retain parsimony-informative sites, which are known to be phylogenetically informative. To test the efficacy of ClipKIT, we examined the accuracy and support of phylogenies inferred from 14 different alignment trimming strategies, including those implemented in ClipKIT, across nearly 140,000 alignments from a broad sampling of evolutionary histories. Phylogenies inferred from ClipKIT-trimmed alignments are accurate, robust, and time saving. Furthermore, ClipKIT consistently outperformed other trimming methods across diverse datasets, suggesting that strategies based on identifying and retaining parsimony-informative sites provide a robust framework for alignment trimming.",
    number = "12"
}

@article{Steenwyk_2021,
    author = "Steenwyk, Jacob L. and Buida, Thomas J. and Gon{\c{c}}alves, Carla and Goltz, Dayna C. and Morales, Grace and Mead, Matthew E. and LaBella, Abigail L. and Chavez, Christina M. and Schmitz, Jonathan E. and Hadjifrangiskou, Maria and Li, Yuanning and Rokas, Antonis",
    doi = "10.1101/2021.10.02.462868",
    url = "https://doi.org/10.1101\%2F2021.10.02.462868",
    year = "2021",
    month = "oct",
    journal = "biorxiv",
    publisher = "Cold Spring Harbor Laboratory",
    title = "{BioKIT}: a versatile toolkit for processing and analyzing diverse types of sequence data"
}

@article{10.1093/molbev/msx281,
    author = "Hoang, Diep Thi and Chernomor, Olga and von Haeseler, Arndt and Minh, Bui Quang and Vinh, Le Sy",
    title = "{UFBoot2: Improving the Ultrafast Bootstrap Approximation}",
    journal = "Molecular Biology and Evolution",
    volume = "35",
    number = "2",
    pages = "518-522",
    year = "2017",
    month = "10",
    abstract = "{The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.}",
    issn = "0737-4038",
    doi = "10.1093/molbev/msx281",
    url = "https://doi.org/10.1093/molbev/msx281",
    eprint = "https://academic.oup.com/mbe/article-pdf/35/2/518/24367824/msx281.pdf"
}

@article{10.1093/bioinformatics/btab096,
    author = "Steenwyk, Jacob L and Buida, Thomas J, III and Labella, Abigail L and Li, Yuanning and Shen, Xing-Xing and Rokas, Antonis",
    title = "{PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data}",
    journal = "Bioinformatics",
    volume = "37",
    number = "16",
    pages = "2325-2331",
    year = "2021",
    month = "02",
    abstract = "{Diverse disciplines in biology process and analyze multiple sequence alignments (MSAs) and phylogenetic trees to evaluate their information content, infer evolutionary events and processes and predict gene function. However, automated processing of MSAs and trees remains a challenge due to the lack of a unified toolkit. To fill this gap, we introduce PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, including but not limited to estimation of mutation rate, evaluation of sequence composition biases, calculation of the degree of violation of a molecular clock and collapsing bipartitions (internal branches) with low support.To demonstrate the utility of PhyKIT, we detail three use cases: (1) summarizing information content in MSAs and phylogenetic trees for diagnosing potential biases in sequence or tree data; (2) evaluating gene–gene covariation of evolutionary rates to identify functional relationships, including novel ones, among genes and (3) identify lack of resolution events or polytomies in phylogenetic trees, which are suggestive of rapid radiation events or lack of data. We anticipate PhyKIT will be useful for processing, examining and deriving biological meaning from increasingly large phylogenomic datasets.PhyKIT is freely available on GitHub (https://github.com/JLSteenwyk/PhyKIT), PyPi (https://pypi.org/project/phykit/) and the Anaconda Cloud (https://anaconda.org/JLSteenwyk/phykit) under the MIT license with extensive documentation and user tutorials (https://jlsteenwyk.com/PhyKIT).Supplementary data are available at Bioinformatics online.}",
    issn = "1367-4803",
    doi = "10.1093/bioinformatics/btab096",
    url = "https://doi.org/10.1093/bioinformatics/btab096",
    eprint = "https://academic.oup.com/bioinformatics/article-pdf/37/16/2325/39948152/btab096.pdf"
}

@article{eaton_toytree_2020,
    author = "Eaton, Deren A. R.",
    title = "Toytree: {A} minimalist tree visualization and manipulation library for {Python}",
    volume = "11",
    doi = "10.1111/2041-210X.13313",
    journal = "Methods in Ecology and Evolution",
    year = "2020",
    pages = "187--191"
}

@article{10.1093/molbev/msaa015,
    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",
    title = "{IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era}",
    journal = "Molecular Biology and Evolution",
    volume = "37",
    number = "5",
    pages = "1530-1534",
    year = "2020",
    month = "02",
    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.}",
    issn = "0737-4038",
    doi = "10.1093/molbev/msaa015",
    url = "https://doi.org/10.1093/molbev/msaa015",
    eprint = "https://academic.oup.com/mbe/article-pdf/37/5/1530/33386032/msaa015.pdf"
}

@article{Kalyaanamoorthy2017,
    author = "Kalyaanamoorthy, Subha and Minh, Bui Quang and Wong, Thomas K F and von Haeseler, Arndt and Jermiin, Lars S",
    type = "Journal Article",
    title = "ModelFinder: fast model selection for accurate phylogenetic estimates",
    journal = "Nature Methods",
    number = "6",
    doi = "10.1038/nmeth.4285",
    volume = "14",
    pages = "587--589",
    url = "https://doi.org/10.1038/nmeth.4285",
    year = "2017",
    abstract = "ModelFinder is a fast model-selection method that greatly improves the accuracy of phylogenetic estimates.",
    issn = "1548-7105",
    DA = "2017/06/01"
}

@article{Zhang2018,
    author = "Zhang, Chao and Rabiee, Maryam and Sayyari, Erfan and Mirarab, Siavash",
    type = "Journal Article",
    title = "ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees",
    journal = "BMC Bioinformatics",
    number = "6",
    doi = "10.1186/s12859-018-2129-y",
    volume = "19",
    pages = "153",
    url = "https://doi.org/10.1186/s12859-018-2129-y",
    year = "2018",
    abstract = "Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one of the leading methods for inferring species trees from gene trees while accounting for gene tree discordance. ASTRAL uses dynamic programming to search for the tree that shares the maximum number of quartet topologies with input gene trees, restricting itself to a predefined set of bipartitions.",
    issn = "1471-2105",
    DA = "2018/05/08"
}