:: DESCRIPTION
RevBayes provides an R-like environment for evolutionary analysis using Bayesian inference and graphical models
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Höhna, S., Heath, T. A., Boussau, B., Landis, M. J., Ronquist, F., Huelsenbeck, J. P. (2014).
Probabilistic graphical model representation in phylogenetics.
Systematic Biology 63:753–771.
:: DESCRIPTION
FFP is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.
::DEVELOPER
Gregory E. Sims , Sung-Hou Kim
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Proc Natl Acad Sci U S A. 2011 May 17;108(20):8329-34. doi: 10.1073/pnas.1105168108. Epub 2011 May 2.
Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs).
Sims GE, Kim SH.
:: DESCRIPTION
BADGER (Bayesian Analysis to Describe Genomic Evolution by Rearrangement) is a free software package for the Bayesian analysis of phylogenies. The package includes programs for analyzing genome arrangements including mitochondrial DNA The main program uses a variety of Metropolis-Hastings proposal mechanisms to sample from the joint posterior distribution of phylogenetic trees using a model of evolution by reversals of the genomic arrangement. Other programs in the distribution help in analysis of the sampled trees and clades.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
CR_Pipeline is a software to solve the Character Removal (CR) Problem for the Multistate Perfect Phylogeny Problem
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug;8(4):912-7. doi: 10.1109/TCBB.2011.27.
Extensions and improvements to the chordal graph approach to the multistate perfect phylogeny problem.
Gysel R, Gusfield D.
:: DESCRIPTION
multperf is a programs used to generate the empirical results on the missing data problem for an arbitrary, but fixed (at input) number of states
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Comput Biol. 2010 Mar;17(3):383-99. doi: 10.1089/cmb.2009.0200.
The Multi-State Perfect Phylogeny Problem with missing and removable data: solutions via integer-programming and chordal graph theory.
Gusfield D.
:: DESCRIPTION
EPoS is a modular software framework for phylogenetic analysis and visualization. Existing phylogenetic software can be split into two groups. Algorithmic packages that provide computational methods for a specific problem, and visualization tools to analyse results. Many algorithmic tools lack in us ability, as they are often command line based, while visualizations often suffer from poor graphical user interfaces.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
EPoS: a modular software framework for phylogenetic analysis
Thasso Griebel; Malte Brinkmeyer; Sebastian Bocker
Bioinformatics , 24(20):2399-2400 2008; doi: 10.1093/bioinformatics/btn364
:: DESCRIPTION
The PATHGROUPS program optimizes the gene order at ancestral nodes of a given phylogeny, given the order in modern genomes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citaion
On the PATHGROUPS approach to rapid small phylogeny.
Zheng C, Sankoff D.
BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S4.
:: DESCRIPTION
GPX (Gene Phylogeny eXplorer) is a web-based tool that facilitates comparative genome analysis of different species. GPX displays results as an interactive map that allows users to explore and interpret genomic data representing gene evolution. It allows the visualization of consensus and conflicting evolutionary histories of genes.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nahar, Neha, Poptsova, Maria S., Hamel, Lutz, and Gogarten, J. Peter (2007)
GPX: A Tool for the Exploration and Visualization of Genome Evolution.
Proceedings of the IEEE 7th International Symposium on Bioinformatics & Bioengineering (BIBE07) Boston, pp1338 – 1342,
:: DESCRIPTION
POPE is a tool to aid high-throughput phylogenetic analysis.POPE provides an integrated platform for automatic ortholog identification. Intermediate steps can be visualized, modified and analyzed in order to assess and improve the underlying quality of orthology and paralogy assignments.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2008 Dec 1;24(23):2778-9. Epub 2008 Oct 10.
POPE–a tool to aid high-throughput phylogenetic analysis.
Juliusdottir T, Pettersson F, Copley RR.
:: DESCRIPTION
ALIFRITZ performs statistical multiple alignment and phylogeny reconstruction simultaneously. It implements a strategy based on simulated annealing which makes use of these models to infer a phylogenetic tree for a set of DNA or protein sequences together with the sequences’ indel history, i.e. their multiple alignment augmented with information about the positioning of insertion and deletion events in the tree.
::DEVELOPER
the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Roland Fleißner, Dirk Metzler and Arndt von Haeseler,
Simultaneous Statistical Multiple Alignment and Phylogeny Reconstruction.
Syst. Biol., 54, 548-561
