Moleculaire biologie
Sinds de intrede van de moleculaire biologie in de schimmel-community is het gebruik van software steeds belangrijker geworden om de groei van data bij te benen.
Het genereren van data is één, maar daarna volgt de analyse van al deze data. Whole genome sequencing heeft de behoefte aan goede software alleen maar vergroot.
De hoeveelheid software voor fylogenie is groot, maar duidelijk is, dat sommige software-pakketten nu als standaard worden gebruikt.
Muscle
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Nucleic Acids Res. 32(5):1792-1797 [http://www.ncbi.nlm.nih.gov/pubmed/15034147].MAFFT
Katoh K, Standley D.M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013 Apr;30(4):772-80. doi: 10.1093/molbev/mst010. Epub 2013 Jan 16 [https://www.ncbi.nlm.nih.gov/pubmed/23329690#].ClustalW
Madeira F, Park YM, Lee J, et al. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Research. 2019 Jul;47(W1):W636-W641. DOI: 10.1093/nar/gkz268 [http://europepmc.org/abstract/MED/30976793].MEGA7
Sudhir Kumar, Glen Stecher, Koichiro Tamura (2016). MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. [https://www.megasoftware.net/pdfs/KumarStecher16.pdf]MEGA X
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018). MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. [https://www.megasoftware.net/pdfs/kumar_stecher_2018.pdf]IQ-tree
L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol., 32:268-274. [https://doi.org/10.1093/molbev/msu300].RaxML
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014 May 1; 30(9): 1312–1313 [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998144/#].MrBayes
Huelsenbeck, J.P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
Ronquist, F., and J.P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
Ronquist, F., M. Teslenko, P. van der Mark, D.L. Ayres, A. Darling, S. Höhna, B. Larget, L. Liu, M.A. Suchard, and J.P. Huelsenbeck. 2012. MRBAYES 3.2: Efficient Bayesian phylogenetic inference and model selection across a large model space. Syst. Biol. 61:539-542. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329765/]FastTree
Price M.N., Dehal P.S., Arkin A.P. (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009 Jul;26(7):1641-50. doi: 10.1093/molbev/msp077. Epub 2009 Apr 17 [https://www.ncbi.nlm.nih.gov/pubmed/19377059#].FigTree
License: GPL
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.Sequence Matrix
Vaidya G, Lohman D.J., Meier R. (2011) SequenceMatrix: concatenation software for the fast assembly of multi‐gene datasets with character set and codon information. Cladistics 2011; 27(2):171-180 [https://doi.org/10.1111/j.1096-0031.2010.00329.x].MatGAT
Campanella J.J., Bitincka L., Smalley J. (2003) MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences. BMC Bioinformatics. 2003; 4: 29 [https://dx.doi.org/10.1186%2F1471-2105-4-29].SATé
Liu, K., T.J. Warnow, M.T. Holder, S. Nelesen, J. Yu, A. Stamatakis, and C.R. Linder (2012) SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees. Systematic Biology. 61(1):90-106 [https://doi.org/10.1093/sysbio/syr095].GBlocks
Talavera, G., and Castresana, J. (2007). Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56, 564-577 [https://doi.org/10.1080/10635150701472164].
