Bibliography¶
Note
If you use auto-phylo, please cite these publications:
H. López-Fernández; M. Pinto; C.P. Vieira; P. Duque; M. Reboiro-Jato; J. Vieira (2023) Auto-phylo: A Pipeline Maker for Phylogenetic Studies. 17th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2023. Guimarães, Portugal. 12 - July
H. López-Fernández; M. Pinto; C. P. Vieira; P. Duque; M. Reboiro-Jato; J. Vieira (2024) auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels and identification of positively selected amino acid sites. Journal of Integrative Bioinformatics. Volume 21(2), Article Number 20230046. ISSN: 1613-4516
- López-Fernández, H., et al., SEDA: a desktop tool suite for FASTA files processing. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2020. 19(3): p. 1850-1860.
- Sievers, F. and D.G. Higgins, Clustal omega. Current protocols in bioinformatics, 2014. 48(1): p. 3.13. 1-3.13. 16.
- Rice, P., I. Longden, and A. Bleasby, EMBOSS: the European molecular biology open software suite. Trends in genetics, 2000. 16(6): p. 276-277.
- Abascal, F., R. Zardoya, and M.J. Telford, TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic acids research, 2010. 38(suppl_2): p. W7-W13.
- Price, M.N., P.S. Dehal, and A.P. Arkin, FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Molecular biology and evolution, 2009. 26(7): p. 1641-1650.
- Bettisworth, B. and A. Stamatakis, Root Digger: a root placement program for phylogenetic trees. BMC bioinformatics, 2021. 22(1): p. 1-20.
- Darriba, D., et al., jModelTest 2: more models, new heuristics and parallel computing. Nature methods, 2012. 9(8): p. 772-772.
- Huelsenbeck, J.P. and F. Ronquist, MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 2001. 17(8): p. 754-755.
- Kumar, S., et al., MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis. Bioinformatics, 2012. 28(20): p. 2685-2686.
- Notredame, C., D.G. Higgins, and J. Heringa, T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of molecular biology, 2000. 302(1): p. 205-217.