:: DESCRIPTION
Unrooted is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). Trees are drawn in an unrooted way, that is, using a circular shape, with labels aligned with terminal branches.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Treevolution is a Java tool for the representation and exploration of phylogenetic trees that facilitates visual analysis. There are several useful tools to visualize phylogenetic trees, but their level of interaction is usually low, especially in the case of radial representations. Highly interactive visualizations can improve the exploration and understanding of phylogenetic trees. Treevolution implements strategies to interact with phylogenetic trees in order to allow a more thorough analysis by users.
::DEVELOPER
The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Santamaría R. and Therón, R.
Treevolution: visual analysis of phylogenetic trees.
Bioinformatics, 2009, 25, 1970-1971
:: DESCRIPTION
Ktreedist is a computer program written in Perl that calculates the minimum branch length distance from one phylogenetic tree to another, providing a measure of the difference in topology and relative branch lengths (shape) between two trees
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Soria-Carrasco, V., Talavera, G., Igea, J., and Castresana, J. (2007).
The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees.
Bioinformatics 23, 2954-2956.
:: DESCRIPTION
SICLE (Sister Clade Extractor) is an easy to use, adaptable, and high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
SICLE: A high-throughput tool for extracting evolutionary relationships from phylogenetic trees
Dan DeBlasio, Jennifer Wiscaver
Genomics arXiv:1303.5785
:: DESCRIPTION
SSA is a program for inferring maximum likelihood phylogenies from DNA sequences. Two versions of the program are available: one which assumes a molecular clock and one which does not make this assumption. The method for searching the space of trees for the ML tree is based on a simulated-annealing type algorithm and is described in the reference above. The program implements Felsenstein’s F84 model of nucleotide substitution and associated sub-models. The program estimates the ML tree and branch lengths, and can optionally estimate the transversion/transversion ratio. Upon termination, the program returns the k trees of highest likelihood found during the search, where k can be set by the user.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Salter, L. and D. Pearl. 2001.
Stochastic Search Strategy for Estimation of Maximum Likelihood Phylogenetic Trees,
Systematic Biology 50(1): 7-17.
:: DESCRIPTION
SSAMK uses a stochastic search algorithm for estimation of maximum likelihood phylogenetic trees for morphological data
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Syst Biol. 2001 Nov-Dec;50(6):913-25.
A likelihood approach to estimating phylogeny from discrete morphological character data.
Lewis PO.
:: DESCRIPTION
MY-CLOSURE is a Java program for computing a phylogenetic network from a collection of phylogenetic trees.
::DEVELOPER
The UEA Computational Biology Laboratory at the University of East Anglia (UEA)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
S. Grunewald, K. T. Huber and Q. Wu,
2 Novel Closure Rules for Constructing Phylogenetic Super-networks,
Bulletin of Mathematical Biology, 70: 1906-1924, 2008
:: DESCRIPTION
TreeLign is automatic update of 16s rRNA phylogenetic tree and multiple sequence alignment in metagenomics
::DEVELOPER
UCF Computational Biology and Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Given a newick binary tree T and its correpsonding multiple sequence alignemnt A of size n x m, where n is the number of leaf nodes in T and m is the length of the alignment, FitchAln generates a (n-1) x (m+1) Fitch score matrix representing the (Maximum Parsimony) number of mutations for each site for each internal node.
::DEVELOPER
UCF Computational Biology and Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
