Note that for large data files, timeouts may occur due to the limited resources of the hosting environment.

PhyloDendron

PhyloDendron.rocks allows users to conduct phylogenetic analyses that normally rely on command-line tools and scripting environments


Tree Inference

Bayesian Inference

Probabilistic method for tree inference using MCMC

Tools: MrBayes

Parsimony

Finds the tree requiring the fewest evolutionary changes

Tools: MPBoot

Maximum Likelihood

Evaluates trees based on probability of observed data under evolutionary models

Tools: IQ-TREE

Distance Methods

Builds trees from pairwise distances from a multiple sequence alignment

Tools: Biopython's NJ and UPGMA

Sequence Alignment

MUSCLE

Multiple sequence alignment

Tool: MUSCLE (v5)

MAFFT

Multiple sequence alignment

Tool: MAFFT (v7)

Clustal Omega

Multiple sequence alignment for large sequences

Tool: Clustal Omega

Other Tools

Newick Tree Viewer

Visualize Newick trees

Tool: PhyloCanvas

Conversion

Convert between different sequence file formats

Tool: BioPython SeqIO

Newick Tree Viewer

Paste a Newick string to generate a visualization

Or upload a Newick file (.nwk, .tree, .tre, .txt)





Citations:

Phylocanvas.gl: A WebGL-powered JavaScript library for large tree visualisation.

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

Sequence Alignment using MUSCLE v5

Upload unaligned sequences (FASTA)






Citations:
Edgar, R.C. (2022) MUSCLE v5. https://doi.org/10.1101/2021.06.20.449169

Sequence Alignment using MAFFT

Upload unaligned sequences (FASTA)


Alignment Strategy




Citations:
Kazutaka Katoh, Daron M. Standley, MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Molecular Biology and Evolution, Volume 30, Issue 4, April 2013, Pages 772–780 https://doi.org/10.1093/molbev/mst010

Sequence Alignment (Clustal Omega)

Upload unaligned sequences (FASTA)


Custom Parameters


Clustal Omega uses seeded guide trees and HMM profile-profile techniques to provide high-scale alignments.



Citations:
Madeira F, Madhusoodanan N, Lee J, et al. The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024. Nucleic Acids Research. 2024 Jul;52(W1):W521-W525 https://doi.org/10.1093/nar/gkae241

Bayesian Inference

Upload aligned sequences (FASTA or NEXUS)


Custom Parameters



Or upload an existing MrBayes consensus tree file (.tre, .con.tre)





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, UPGMA and NJ use IQ-TREE to select the best-fit evolutionary model and compute a phylogenetic distance matrix.

Upload aligned sequences (FASTA)



Select method





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

Maximum Parsimony (MPBoot)

Construct phylogenetic trees using fast maximum parsimony with bootstrap replicates.

Upload aligned sequences (FASTA)


Parameters




Citations:

D.T. Hoang, L.S. Vinh, T. Flouri, A. Stamatakis, A. von Haeseler, and B.Q. Minh (2018) MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC Evol. Biol., 18, 11. https://doi.org/10.1186/s12862-018-1131-3

Maximum Likelihood (IQ-TREE)

IQ-TREE uses ModelFinder to pick the best substitution model and builds an ML tree.

Upload aligned sequences (FASTA)


Parameters




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/

Convert Sequence File Formats

Upload sequence file

Molecule type



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