Authors, References and Citation

Here you will find all the useful metadata about people and dependencies linked to AMPLIPIPER

Table of contents

Developers

Contributors

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References

Software

  • Pigz: Adler, M., https://github.com/madler/pigz
  • Chopper: Wouter De Coster, Rosa Rademakers, NanoPack2: population-scale evaluation of long-read sequencing data, Bioinformatics, Volume 39, Issue 5, May 2023, btad311, https://doi.org/10.1093/bioinformatics/btad311
  • MAFFT: Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772-780. doi: 10.1093/molbev/mst010
  • IQtree: 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. doi: 10.1093/molbev/msu300
  • Astral: Zhang, C., Rabiee, M., Sayyari, E., & Mirarab, S. (2018). ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics, 19(1), 153. doi: 10.1186/s12859-018-2129-4
  • ASAP: Puillandre N, Brouillet S, Achaz G. ASAP: assemble species by automatic partitioning. Mol Ecol Resour. 2021; 21: 609–620. https://doi.org/10.1111/1755-0998.13281
  • GNU Parallel: Tange, O. (2011). GNU Parallel - The Command-Line Power Tool. ;login: The USENIX Magazine, 36(1), 42-47.
  • BLAST: Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403-410. doi: 10.1016/S0022-2836(05)80360-2

Python Packages

  • Biopython: Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A.,… & de Hoon, M. J. L. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422-1423. doi: 10.1093/bioinformatics/btp163
  • Edlib: Šošić, M., & Šikić, M. (2017). Edlib: a Python library for fast and efficient edit distance calculation. Bioinformatics, 33(11), 1741-1742. doi: 10.1093/bioinformatics/btx053
  • CairoSVG: Kozea, https://github.com/Kozea/CairoSVG
  • PyMSAviz: https://github.com/moshi4, https://github.com/moshi4/pyMSAviz
  • ETE3: Huerta-Cepas, J., Serra, F., & Bork, P. (2016). ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Molecular Biology and Evolution, 33(6), 1635-1638. doi: 10.1093/molbev/msw046
  • Pandas: McKinney, W. (2010). Data structures for statistical computing in Python. Proceedings of the 9th Python in Science Conference, 51-56.
  • Matplotlib: Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. Computing in Science & Engineering, 9(3), 90-95. doi: 10.1109/MCSE.2007.55
  • BeautifulSoup: Richardson, L. (2007). Beautiful Soup. Crummy, 1-12.
  • SciPy: Virtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Reddy, T., Cournapeau, D.,… & SciPy 1.0 Contributors. (2020). SciPy 1.0: Fundamental Algorithms for Scientific Computing. arXiv preprint arXiv:2006.12345.

R Packages

  • R-base: R Core Team. (2021). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing.
  • Bioconductor-ggtree: Yu, G., Smith, D. K., Zhu, H., Guan, Y., & Lam, T. T. Y. (2017). ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution, 8(1), 28-36. doi: 10.1111/2041-210X.12628
  • R-tidyverse: Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L. D., François, R.,… & Yutani, H. (2019). Welcome to the tidyverse. Journal of Open Source Software, 4(43), 1686. doi: 10.21105/joss.01686
  • Bioconductor-treeio: Li, M., & Ma, J. (2019). treeio: an R package for phylogenetic tree input/output and manipulation. Bioinformatics, 35(11), 1939-1941. doi: 10.1093/bioinformatics/btz024
  • R-phytools: Revell, L. J. (2012). phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3(2), 217-223. doi: 10.1111/j.2041-210X.2011.00169.x
  • R-ape: Paradis, E., Claude, J., & Strimmer, K. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20(2), 289-290. doi: 10.1093/bioinformatics/btg412
  • R-treedist: FitzJohn, R. G. (2012). Diversitree: comparative phylogenetic analyses of diversification in R. Methods in Ecology and Evolution, 3(6), 1084-1092. doi: 10.1111/j.2041-210X.2012.00234.x
  • R-reshape2: Wickham, H. (2007). Reshaping data with the reshape package. Journal of Statistical Software, 21(12), 1-20. doi: 10.18637/jss.v021.i12

Citation

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