References
Andrews, S. (2010). FastQC A Quality Control tool for High Throughput Sequence Data . http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A., & Pevzner, P. A. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology: A Journal of Computational Molecular Cell Biology , 19 (5), 455–477. https://doi.org/10.1089/cmb.2012.0021
Borowiec, M. L. (2016). AMAS: a fast tool for alignment manipulation and computing of summary statistics. In PeerJ (Vol. 4, p. e1660). https://doi.org/10.7717/peerj.1660
Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., Duchêne, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., Kühnert, D., De Maio, N., Matschiner, M., Mendes, F. K., Müller, N. F., Ogilvie, H. A., du Plessis, L., Popinga, A., Rambaut, A., Rasmussen, D., Siveroni, I., … Drummond, A. J. (2019). BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Computational Biology , 15 (4), e1006650. https://doi.org/10.1371/journal.pcbi.1006650
Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. In Bioinformatics (Vol. 34, Issue 17, pp. i884–i890). https://doi.org/10.1093/bioinformatics/bty560
Darriba, D., Flouri, T., & Stamatakis, A. (2018). The state of software for evolutionary biology. Molecular Biology and Evolution ,35 (5), 1037–1046. https://doi.org/10.1093/molbev/msy014
DeSalle, R., Tessler, M., & Rosenfeld, J. (2020). Phylogenetic Programs and Websites. In Phylogenomics (pp. 213–222). CRC Press. https://doi.org/10.1201/9780429397547-20
Faircloth, B. C. (2016). PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics , 32 (5), 786–788. https://doi.org/10.1093/bioinformatics/btv646
Grealey, J., Lannelongue, L., Saw, W.-Y., Marten, J., Méric, G., Ruiz-Carmona, S., & Inouye, M. (2022). The Carbon Footprint of Bioinformatics. Molecular Biology and Evolution , 39 (3). https://doi.org/10.1093/molbev/msac034
Hutter, C. R., Cobb, K. A., Portik, D. M., Travers, S. L., Wood, P. L., Jr, & Brown, R. M. (2022). FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. Molecular Ecology Resources , 22 (3), 1100–1119. https://doi.org/10.1111/1755-0998.13517
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., Suh, A., Weber, C. C., da Fonseca, R. R., Li, J., Zhang, F., Li, H., Zhou, L., Narula, N., Liu, L., … Zhang, G. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds.Science , 346 (6215), 1320–1331. https://doi.org/10.1126/science.1253451
Katoh, K., Misawa, K., Kuma, K.-I., & Miyata, T. (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research , 30 (14), 3059–3066. https://doi.org/10.1093/nar/gkf436
Köster, J. (2016). Rust-Bio: a fast and safe bioinformatics library.Bioinformatics , 32 (3), 444–446. https://doi.org/10.1093/bioinformatics/btv573
Kozlov, A. M., Darriba, D., Flouri, T., Morel, B., & Stamatakis, A. (2019). RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics ,35 (21), 4453–4455. https://doi.org/10.1093/bioinformatics/btz305
Kück, P., & Longo, G. C. (2014). FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies. Frontiers in Zoology , 11 (1), 81. https://doi.org/10.1186/s12983-014-0081-x
Lemoine, F., & Gascuel, O. (2021). Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows. NAR Genomics and Bioinformatics , 3 (3), lqab075. https://doi.org/10.1093/nargab/lqab075
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.Molecular Biology and Evolution , 37 (5), 1530–1534. https://doi.org/10.1093/molbev/msaa015
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution ,32 (1), 268–274. https://doi.org/10.1093/molbev/msu300
Oliveros, C. H., Field, D. J., Ksepka, D. T., Barker, F. K., Aleixo, A., Andersen, M. J., Alström, P., Benz, B. W., Braun, E. L., Braun, M. J., Bravo, G. A., Brumfield, R. T., Chesser, R. T., Claramunt, S., Cracraft, J., Cuervo, A. M., Derryberry, E. P., Glenn, T. C., Harvey, M. G., … Faircloth, B. C. (2019). Earth history and the passerine superradiation. Proceedings of the National Academy of Sciences of the United States of America , 116 (16), 7916–7925. https://doi.org/10.1073/pnas.1813206116
Perkel, J. M. (2020). Why scientists are turning to Rust. Nature ,588 (7836), 185–186. https://doi.org/10.1038/d41586-020-03382-2
Román-Palacios, C. (2023). The ‘phruta’ R package and ‘salphycon’ shiny app: increasing access, reproducibility, and transparency in phylogenetic analyses. In bioRxiv (p. 2023.01.11.523621). https://doi.org/10.1101/2023.01.11.523621
Steenwyk, J. L., & Rokas, A. (2019). Treehouse: a user-friendly application to obtain subtrees from large phylogenies. BMC Research Notes , 12 (1), 541. https://doi.org/10.1186/s13104-019-4577-5
Suchard, M. A., Lemey, P., Baele, G., Ayres, D. L., Drummond, A. J., & Rambaut, A. (2018). Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution , 4 (1), vey016. https://doi.org/10.1093/ve/vey016
Yang, Z. (2015). The BPP program for species tree estimation and species delimitation. Current Zoology , 61 (5), 854–865. https://doi.org/10.1093/czoolo/61.5.854