Parsimony

TreeFitter is designed as an accessible and handy application for parsimony-based tree fitting. TreeFitter is a CLi-based tool that can be used for analyzing problems in historical biogeography, coevolution, and in species tree - gene tree fitting.


Platforms: Windows

This package includes a modified version of dnapars.exe from Phylip 3.6. The orignal dnapars,exe uses a menu for settings of parameters. I changed it into a command-line driven one, called mbetoolbox_dnapars.exe. Then I built a MATLAB interface for it. Within MATLAB, after setting the path, set...


Platforms: Matlab

SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView reads and writes various file formats of DNA and protein sequences and of phylogenetic trees. SeaView drives programs muscle or clustalw for multiple sequence alignment, and...


Platforms: Mac

A xenohistorical expedition to recover artifacts of "the Ancients" takes on a surprisingly human and personal tone in this far-future sci-fi story. Simple Planetfall-like puzzles, thoughtful prose that establishes moods with parsimony. Short but not rushed. Well worth playing.


Platforms: Mac

Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the...


Platforms: Mac

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...


Platforms: Windows

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...


Platforms: Linux

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...


Platforms: Mac

SIMMAP 1.5 is a post tree analysis GUI software package for stochastically mapping mutations on phylogenies. This approach does not rely on parsimony and, therefore, does not suffer some of the serious drawbacks of that method. It uses the "indirect" mutational mapping approach as first developed...


Platforms: Mac