Main Page
Info ab site, libraries used ect.
Newick Tree Viewer
Enter a Newick string to generate a visualization.
Citations:
Eric Talevich, Brandon M. Invergo, Peter J.A. Cock, Brad A. Chapman: Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinformatics 13: 209 (2012). https://doi.org/10.1186/1471-2105-13-209 https://doi.org/10.1186/1471-2105-13-209
Sequence Alignment using MUSCLE
Enter your FASTA format sequences.
Bayesian Inference
Citations:
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.
Altekar, G., S. Dwarkadas, J. P. Huelsenbeck, and F. Ronquist. 2004. Parallel Metropolis-coupled Markov chain
Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20:407-415.
Distance Methods
To construct a tree, both UPGMA and NJ will use IQ-TREE to use select the best evolutionary model and calculate the phylogenetic distance matrix.
Citations:
Thomas K.F. Wong, Nhan Ly-Trong, Huaiyan Ren, Hector Banos, Andrew J. Roger,
Edward Susko, Chris Bielow, Nicola De Maio, Nick Goldman, Matthew W. Hahn,
Gavin Huttley, Robert Lanfear, Bui Quang Minh (2025) IQ-TREE 3: Phylogenomic
Inference Software using Complex Evolutionary Models. Submitted.
https://ecoevorxiv.org/repository/view/8916/
Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg,
Thomas Hamelryck, Frank Kauff, Bartek Wilczyński, Michiel J. L. de Hoon: Biopython: freely available Python
tools for computational molecular biology and bioinformatics. Bioinformatics 25 (11), 1422–1423 (2009).
https://doi.org/10.1093/bioinformatics/btp163
Eric Talevich, Brandon M. Invergo, Peter J.A. Cock, Brad A. Chapman: Bio.Phylo: A unified toolkit
for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinformatics 13:
209 (2012). https://doi.org/10.1186/1471-2105-13-209
https://doi.org/10.1186/1471-2105-13-209
Parsimony
Coming soon.
Maximum Liklihood
Coming soon.
Conversion from a FASTA file to a NEXUS file.
Notes. Will delete!
The current functionality of this page is limited to converting fasta files to nexus files
(the file type MrBayes takes in as input). (The functionality has been tested w/ our aligned fasta files from TP1)
We will eventually add other file conversions. And do more thorough testing including testing other types of molecules (RNA and proteins).
Citations:
Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczyński, Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25 (11), 1422–1423 (2009). https://doi.org/10.1093/bioinformatics/btp163