:: DESCRIPTION
TNT (Tree Analysis using New Technology) is a program for phylogenetic analysis under parsimony , as well as extensive tree handling and diagnosis capabilities.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Giribet G.
“TNT: Tree Analysis Using New Technology.”.
Syst Biol. 2005;54:176-178.
:: DESCRIPTION
DARwin (Dissimilarity Analysis and Representation for Windows) is a software package developed for diversity and phylogenetic analysis on the basis of evolutionary dissimilarities.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Perrier, X., Flori, A. , Bonnot, F. (2003). Data analysis methods.
In: Hamon, P., Seguin, M., Perrier, X. ,Glaszmann, J. C. Ed., Genetic diversity of cultivated tropical plants. Enfield, Science Publishers. Montpellier. pp 43 – 76.
:: DESCRIPTION
PAML (Phylogenetic Analysis by Maximum Likelihood) is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (dN and dS) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use.
PAML-X: A GUI for PAML
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Yang, Z. 2007.
PAML 4: a program package for phylogenetic analysis by maximum likelihood.
Molecular Biology and Evolution 24: 1586-1591
Mol Biol Evol. 2013 Oct 24.
PAMLX: A Graphical User Interface for PAML.
Xu B, Yang Z.
:: DESCRIPTION
BEST (Bayesian Estimation of Species Trees)is a free phylogenetics program to estimate the joint posterior distribution of gene trees and species tree using multilocus molecular data that accounts for deep coalescence but not for other issues such as horizontal transfer or gene duplication.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BEST: Bayesian estimation of species trees under the coalescent model.
Liu L.
Bioinformatics. 2008 Nov 1;24(21):2542-3. doi: 10.1093/bioinformatics/btn484
:: DESCRIPTION
PHAST is a freely available software package for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations.
RPHAST: Phylogenetic Analysis with Space/Time Models… in R
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Brief Bioinform. 2011 Jan;12(1):41-51. doi: 10.1093/bib/bbq072. Epub 2010 Dec 21.
PHAST and RPHAST: phylogenetic analysis with space/time models.
Hubisz MJ1, Pollard KS, Siepel A.
:: DESCRIPTION
Bosque is a distributed software environment oriented to manage the computational resources involved in typical phylogenetic analyses. Bosque has been implemented as a client-server application where the server can execute installed phylogenetic programs (Phylip, PhyML, TreePuzzle, Muscle) and the client manages the results on a local relational database, although it can also execute phylogenetic programs locally, useful when no server is available. The client also performs the graphical visualisation and edition of trees and alignments, providing an environment for the analyses, from the integration of sequences to the printing of a final tree.
::DEVELOPER
Millenium Institute of Oceanography
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Ramírez-Flandes S. & O. Ulloa(2008).
Bosque: Integrated phylogenetic analysis software.
Bioinformatics 24(21):2539-2541; doi: 10.1093/bioinformatics/btn466
:: DESCRIPTION
The “diversitree” package includes a number of comparative phylogenetic methods, mostly focussing on analysing diversification and character evolution.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Richard G. FitzJohn
Diversitree: comparative phylogenetic analyses of diversification in R
Issue Methods in Ecology and Evolution Methods in Ecology and Evolution Volume 3, Issue 6, pages 1084–1092, December 2012
:: DESCRIPTION
“FISHtrees” is a software program:
1) to parse copy numbers of multiple Fluorescence In Situ Hybridization (FISH) probe signals in a single-cell assay;
2) to analyze probe signals across multiple single-cell assays in a patient data file;
3) to model tumorigenesis as a tree of tumor progression paths for a given probe on a given patient data file;
4) to merge multiple tumorigenesis trees to represent multiple probes on a given patient data file;
5) to compute consensus multiple joint tumorigenesis trees representing multiple patient data files into a network as a graph of tumor progression pathways.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gertz EM, et al.
FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe.
PLoS One. 2016 Jun 30;11(6):e0158569. doi: 10.1371/journal.pone.0158569. PMID: 27362268; PMCID: PMC4928784.
Bioinformatics. 2013 Jul 1;29(13):i189-98. doi: 10.1093/bioinformatics/btt205.
Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations.
Chowdhury SA1, Shackney SE, Heselmeyer-Haddad K, Ried T, Schäffer AA, Schwartz R.
:: DESCRIPTION
Armadillo is a workflow platform dedicated to phylogenetic as well as general bioinformatics analysis.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2012;7(1):e29903. doi: 10.1371/journal.pone.0029903. Epub 2012 Jan 11.
Armadillo 1.1: an original workflow platform for designing and conducting phylogenetic analysis and simulations.
Lord E1, Leclercq M, Boc A, Diallo AB, Makarenkov V.
:: DESCRIPTION
phyloExpCM is a Python package to implement experimentally determined codom models of substitution for phylogenetics.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bloom JD.
An experimentally determined evolutionary model dramatically improves phylogenetic fit.
Mol Biol Evol. 2014;31:1956-1978.
