MrBayes 3.2.0
MrBayes is a simple, easy to use application specially designed for the Bayesian estimation of phylogeny.
The program takes as input a character matrix in a NEXUS file format. The output is several files with the parameters that were sampled by the MCMC algorithm. MrBayes can summarize the information in these files for the user.
Price: USD $0.00;
License: Freeware
Platform: Windows 3.x, Windows , All
Seq-Gen 1.3.2
Seq-Gen is a software that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and...
Price: USD $0.00;
License: Freeware
File Size: 281 KB;
Platform: Windows
SeqVerter 2.0.4.3
View automatic DNA sequencer chromatogram files with this tool. SeqVerter is a free sequence file format conversion utility by GeneStudio, Inc. SeqVerter encapsulates a small subset of the features offered by the GeneStudio Pro suite of programs. While the standalone SeqVerter is a simple dialog-based utility, the free SeqVerter component of the GeneStudio Pro suite adds sophisticated viewers and sequence formatting functions, including a...
Phight 1.0
Phight - a phylogeny tree building program Currently, it supports Likelihood method and distance method. This program will includes diagnostic function as a special feature.
DNATREE 1.3
DNATREE is a computer program that simulates the branching of an evolutionary tree, using a model of random branching of lineages. It then evolves a DNA sequence along this tree, and displays the resulting sequences. The user can save the tree and the sequences if they want to use them in other programs. The user can control the expected rate of evolution of the sequences per unit time, and the transition/transversion ratio.
After the tree...
Price: USD $0.00;
License: Freeware
Platform: Windows XP, Windows, Windows Vista , Windows Vista x64,Windows 7,Windows 7 x64
DNATREE for Linux 1.3
DNATREE is a computer program that simulates the branching of an evolutionary tree, using a model of random branching of lineages. It then evolves a DNA sequence along this tree, and displays the resulting sequences. The user can save the tree and the sequences if they want to use them in other programs. The user can control the expected rate of evolution of the sequences per unit time, and the transition/transversion ratio.
After the tree...
Price: USD $0.00;
License: Freeware
Platform: Linux
DNATREE for Mac OS X 1.3
DNATREE is a computer program that simulates the branching of an evolutionary tree, using a model of random branching of lineages. It then evolves a DNA sequence along this tree, and displays the resulting sequences. The user can save the tree and the sequences if they want to use them in other programs. The user can control the expected rate of evolution of the sequences per unit time, and the transition/transversion ratio.
After the tree...
Price: USD $0.00;
License: Freeware
Platform: Mac, Linux
MacGDE for Mac OS 2.4
A set of programs for multiple sequence alignment and analysis. The programs use an expandable user interface which allows the addition of external analysis functions without any rewriting of code. The system supports several data types, nucleic and amino acid sequences, text, and masking sequence, and three forms of color highlighting. The system has several external analysis functions included for such things as automated alignment,...
MSight 3.0.1
MSight is a new vision in Mass Spectrometry Imaging. MSight, created by the Proteome Informatics Group, was specifically developed for the representation of mass spectra along with data from the separation step. The program allows graphical exploration inside huge dataset and gives the scientist access to information that previously was hidden.It provides simple ways to navigate through very large volumes of data, with the capability to...
Unrooted 1.0
Unrooted is a tree drawing software 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.Use of Unrooted:A file selection box allows to select the tree file which then is drawn on the screen. A postscript output of the drawing can be prepared (on Macintosh, the...
ModelGenerator 0.85
Analyze nucleotide substitution model fast and easy.ModelGenerator is a model selection software that selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments. ModelGenerator supports 56 nucleotide and 96 amino acid substitution models.Startup commandjava -jar modelgenerator.jar alignment_file num_gamma_categoriesIf you get a java.lang.OutOfMemory error then increase the amount of memory available to java...
NJPlot 2.3
Create phylogenetic trees with this tool. NJplot is a tree drawing software able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially handy for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.Use of NJPlotAny rooting of the unrooted tree can be interactively specified using the mouse. NJplot...
FigTree 1.3.1
FigTree is a graphical viewer of phylogenetic trees. It is a graphical viewer of phylogenetic trees and as a software for producing publication-ready figures.As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST.FigTree is designed as a graphical viewer of phylogenetic trees and...
Treefinder 1.0
Computes phylogenetic trees from molecular sequences. Treefinder computes phylogenetic trees from molecular sequences. The software infers even large trees by maximum likelihood under a variety of models of sequence evolution. It accepts both nucleotide and amino acid data and takes rate heterogeneity into account.Separate models can be assumed for user-defined data partitions, separate rates, separate edge lengths, separate character...
TreeStat 1.2
Can process a set of trees in a PHYLIP or NEXUS format tree file. TreeStat is an software that can process a set of trees in a PHYLIP or NEXUS format tree file and calculate a number of summary statistics for each. These are saved in a tab-delimited file for analysis in Tracer or statistics packages. A range of summary statistics are included:1. Tree-Balance Statistics. Colless's, B1, N_bar, cherry count.2. Tree shape.Tree height, node...
