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TreeFitter is a utility for phylogenetic tree fitting. It includes parsimony tree search, probability matrix optimization, and bootstrap value estimation. The result trees can be displayed graphically, printed, or saved as Newick, Nexus or other formats. Features * Parsimony tree search * Probability matrix optimization * Nucleotide substitution rate optimization * Bootstrap value estimation * Probability of monophyly and polyphyly * Multiple simultaneous searches (e.g., simultaneous nucleotide substitution rate optimization, partitioned parsimony) * Interactive optimization * Exact calculation of a probability of polyphyly Version 0.10b (14.09.2011) Added parsimony support * Parsimony branches can be created by moving a single, selected terminal node * Parsimony parameters can be specified * Parsimony indices can be specified * Exact addition of a constant to a tree allows for exact calculation of the probability of polyphyly * New command-line parsing code, which should make tree-fitting with TreeFitter more robust * Minor code clean-up and bug fixes Version 0.10a (10.08.2011) Fixed a bug that caused the program to crash while parsing parsimony data in the presence of an extremely large number of bootstrap values Added functionality for calculating the probability of a monophyletic group of taxa as zero. This functionality can be used to check and adjust the priors in phylogenetic studies. Added functionality for calculating the probability of a monophyletic group of taxa as one. This functionality can be used to check and adjust the priors in phylogenetic studies. Improved compatibility with 32-bit and 64-bit Windows versions of TreeFitter Added support for inclusion of alignment data (e.g., amino acid or nucleotide data) in analyses Version 0.10 (06.07.2011) Added compatibility with Mac OS X. Added compatibility with Sun Solaris. Added tree saving functionality for Portable Network Graphics (PNG) format (new format in version 0.9). Added a useful new command line parameter, –explain, which explains the logic of each node in the tree (if applicable). Added the possibility to save trees as Newick, Nexus, NEXUS, or IPT files. Improved compatibility with Windows versions of TreeFitter. Improved compatibility with 32-bit and

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This package contains all tools and programs for the analysis of phylogenetic and co-phylogenetic relationships between tree species distributions and genes. It is designed to be an open-source, accessible and a handy tool for tree fitting. TreeFitter Requirements: The description above is an example usage. You can use this tool when you: – Analyze the relationships between tree species distributions and gene trees and form a model of co-distribution. – Perform parsimony based tree-fitting (if the user needs to do tree-fitting). – Per-form parsimony based tree-fitting and analysis of topologies. – There are a number of additional tools, packages and programs also available in this package that don’t fit this description, they are: – fastMLMP: For analyzing molecular clocks (for the ML protocol). – fastDNAml: For performing phylogenetic inference using the ML protocol. – ParallelizedTreeFitter: For performing tree-fitting on multi-core machines. – ParallelizedTreeFitterML: For performing tree-fitting on multi-core machines. Using the ML protocol. – aml: For computing Bayesian posterior probabilities for a given topology, tree model and alignment. – qtplot: For plotting various aspects of alignment files. – qtplot2: For plotting 2-state and 3-state mutations. – qtplot3: For plotting multiple transitions/transversions. – qtplot4: For plotting more features on an alignment file. – fileLX: For converting text files to various formats. – sp: For performing statistical parsimony on data sets. – tn: For performing both Topological Nerve and Topological Network analysis. – tn4: For performing both Topological Nerve and Topological Network analysis. – nhx2: For performing Neighbor-Joining on data sets. – TreeFitterAssembler: For generating a job, running in parallel, in the GUI/CLi. – TreeFitterAssemblerML: For generating a job, running in parallel, in the GUI/CLi. Using the ML protocol. – TreeFitterAssemblerML2: For generating a job, running in parallel, in the GUI/CLi. – TreeFitterAssemblerMLparallel: For generating a job, running in parallel, in the GUI/CLi. 2f7fe94e24

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TreeFitter allows the user to design, analyze and evaluate hypotheses of relationships in a phylogenetic tree using the parsimony principle. This tool is simple to use, straightforward and free. TreeFitter uses CLi, a command-line interface for UNIX that allows the user to specify the analysis in a step-by-step fashion and to run it on multiple trees that can be specified as inputs. CLi allows for an easy integration with shell scripts, thus allowing automatic generation of trees. It has a graphical user interface. The user interface is able to select among different tree models for each of the input files. The user can choose to use all input files simultaneously or to use specific subsets of the input files. The user is also able to specify the number of trees that will be used for the analysis. He is also able to specify whether more than one constraint will be used. Each constraint will be used in some other resolution. As a result, the user can define one or more individual constraints for the analysis. The user can set the weight of each of the constraints in each of the analyses. The user can also set a model-based constraint for the analysis, which is a constraint that cannot be satisfied with any tree model. In each of the analyses, the user can select to have constraint violation based on the majority rule as the output. This output is displayed as a PDF output file. Each constraint will be used in some other resolution in the analysis. Thus, if, for example, in a partial constraint, the best tree in the partial constraint will always be the resolution to the edge but the overall analysis does not favor that resolution, this is not a violation, but instead a resolution for which no better resolution for that constraint is available. TreeFitter can also be used with outgroups. Clustering is allowed, and several clustering algorithms are available. An outgroup distance matrix can be used. TreeFitter Features: It is free and can be used for research as well as for teaching. It is accessible in any major operating system (Linux, Windows, Mac). The user can set the default resolution for trees with missing data in cases where there is disagreement between conflicting constraints or between conflicting and model-based constraints. The user can specify which tree is used as a starting point for the analysis. A special feature of TreeFitter is that it checks if there are missing data in the input (the presence of gaps in the sequence alignment), and then

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TreeFitter is a CLi-based tool for parsimony-based maximum likelihood tree fitting and, in addition, for tuning of models of sequence evolution (and by extension, for nucleotide substitution models). In TreeFitter, an input tree is parameterized with the species of interest, morphological (or other) data (sites/individuals) and ancestral areas. Site- and gene-based distances are then calculated between all possible pairs of taxa, and the fit of any phylogenetic model to the data is calculated from a weighted sum of the distances (i.e. the distance matrix) according to their relative cost of insertion and deletion (i.e. the weighting vector). As such, TreeFitter employs a weighted parsimony framework for phylogenetic model fitting, following currently employed maximum likelihood approaches (e.g. Felsenstein, 2005). The model parameters can be adjusted according to the criteria of the model complexity – an important advantage of TreeFitter compared to the other CLi tools for model fitting is the possibility of variable rates among clades of a tree. In fact, rates and rate-change are estimated for all branches of a tree, or branches of a subtree. For example, Hillis et al. (2005) and Kumar et al. (2005) estimated the rates of rate in various lineages across the human mitochondrial and human D-loop sequences, respectively. As in other approaches (e.g. Yang and Sinai, 2004), the rates estimated by TreeFitter can be considered as a measure of the relative rate of genetic evolution in various lineages. Also, each site can be treated as the potential site for insertion/deletion (indel) events, depending on the indel cost and, as such, each indel at each site can be considered as a distinct model parameter, and the indel cost function can be adjusted. The indel cost in TreeFitter is approximated by the product of the indel frequencies and estimated indel costs. The indel cost is not limited to the pairwise site-based distance function, and can also be considered as a function of branch lengths, when distances are used for model fitting (see Gill et al., 2003). Another important difference between TreeFitter and the most advanced methods is that the entire tree can be parameterized in this way and the weighting vector can be created off-line for a user-defined set of data. As such, the output of this method can be used

System Requirements For TreeFitter:

Minimum: OS: Windows Vista or Windows XP SP2 or later (64-bit edition only) CPU: Intel Pentium 4 3.0 GHz (or AMD Athlon XP 2400+) or higher (64-bit edition only) RAM: 1 GB RAM or higher DirectX: DirectX 9.0c or higher Graphics: Nvidia GeForce 8600 or ATI Radeon X1900 Hard Drive: 1 GB of free space Sound Card: Microsoft Sound Card Recommended: OS: Windows Vista or Windows XP SP



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