Phylogenetic Tree Construction

Phylogenetic Comparative Assembly New Patrick Schwientek & Peter Husemann 

Phylogenetic Comparative Assembly is a handy and easy to use application designed to help you generate a phylogenetic tree from reference genomes.

After loading the reference genomes, the application builds the config adjacency graph and the layouting contigs. The output layout graph can be displayed using neato of the GraphViz. Freeware download of Phylogenetic Comparative Assembly New, size 0 b.


   

AcidMiner 02.beta acidminer.sourceforge.net 

Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.. Freeware download of AcidMiner 02.beta, size 3979.73 Mb.

ParsInsert 1.04 parsinsert.sourceforge.net 

ParsInsert efficiently produces both a phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis. This is a C++ implementation of the Parsimonious Insertion algorithm.. Freeware download of ParsInsert 1.04, size 53.70 Kb.

tax2tree 1.0 tax2tree.sourceforge.net 

Tools for decorating taxonomy information on to a phylogenetic tree. Freeware download of tax2tree 1.0, size 31.84 Kb.

Previous Project 1.0 Parsinsertx 

ParsInsert efficiently produces both a phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis. This is a C++ implementation of the Parsimonious Insertion algorithm.

Previous Project 1.0 License - GNU General Public License (GPL). Freeware download of Previous Project 1.0, size 0 b.

wxGeneee b wxgenebee.sourceforge.net 

The set of tools for biopolymer sequence analysis togetherwith GUI to work with biopolymer sequence databases.The tools include pairwise and multiple alignment, philogenetic tree construction and other.. Freeware download of wxGeneee b, size 1.11 Mb.

codonPhyML 1.00.201212.16 Codonphyml 

codonPhyML uses Markovian codon models of evolution in phylogeny reconstruction. Given a set of species characterized by their DNA sequences as input, codonPhyML will return the phylogenetic tree that best describes their evolutionary relationship.

Markovian codon models of evolution: Goldman & Yang 1994, Muse & Gaut 1994, Kosiol. Freeware download of codonPhyML 1.00.201212.16, size 4.95 Mb.

wxGenebee b Wxgenebee 

The set of tools for biopolymer sequence analysis togetherwith GUI to work with biopolymer sequence databases.The tools include pairwise and multiple alignment, philogenetic tree construction and other.

wxGenebee b License - GNU General Public License (GPL). Freeware download of wxGenebee b, size 1.11 Mb.

TREECON for Windows 1.3b Yves Van de Peer 

TREECON is a software package developed primarily for the construction and drawing of phylogenetic trees on the basis of evolutionary distances inferred from nucleic and amino acid sequences. The evolutionary distance is computed for all pairs of organisms (or sequences) and a phylogenetic tree is inferred by considering the relationship between. Free download of TREECON for Windows 1.3b, size 2.29 Mb.

Treefinder March 2011 Gangolf Jobb 

The TREEFINDER application computes phylogenetic trees from molecular sequences. The program 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. Free download of Treefinder March 2011, size 0 b.

GenNon-h 1.0 Gennonh 

A number of software packages are available to
generate DNA MSAs evolved under
continuous-time Markov processes on phylogenetic trees. On the other hand,
methods of simulating the DNA MSA directly from the transition matrices
do not exist. Moreover, existing software restricts to
the time-reversible models and it is not. Freeware download of GenNon-h 1.0, size 4.22 Mb.

UGENE for Windows 1.9.8 Unipro 

UGENE is a free cross-platform genome analysis suite.
<b>
Main features:</b>

* Multiple sequence alignment using MUSCLE 3,4 and KAlign;
* HMM profiles build and search, based on the source of HMMER 2 and HMMER 3;
* PCR Primers design using Primer 3;
* Protein secondary structure prediction using. Free download of UGENE for Windows 1.9.8, size 20.64 Mb.

HyperProtein 1.0 Hypercube, Inc. 

HyperProtein is Hypercube, Inc.'s new product focusing on the computational science associated with protein sequences. The product includes the analysis of one-dimensional protein sequences as well as the analysis of consequent three-dimensional protein structures. In particular, the relationship between sequence and structure is a fundamental. Free download of HyperProtein 1.0, size 45.20 Mb.

Unipro UGENE 1. 9. 2002 Unipro, Russia 

UGENE is a free cross-platform genome analysis suite.
It works perfectly on Windows, Mac OS or Linux and requires only a few clicks to install.

Main features:

Integrated tools

-Multiple sequence alignment using MUSCLE 3, KAlign, Clustal;
-HMM profiles build and search, based on the source of. Freeware download of Unipro UGENE 1. 9. 2002, size 16.47 Mb.

Geneious PRO x64 5. 5. 2005 Biomatters Ltd 

Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis, contig assembly, primer design and cloning, access to. Free download of Geneious PRO x64 5. 5. 2005, size 31.46 Mb.

Geneious PRO for Vista 4. 7. 2006 Biomatters Ltd 

Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis, contig assembly, primer design and cloning, access to. Free download of Geneious PRO for Vista 4. 7. 2006, size 31.46 Mb.

Unipro UGENE 64-bit 1.11.4 Unipro 

Unipro UGENE 64-bit is a free visual software solution for DNA and protein sequence analysis. UGENE provides customizable tools for visualization, analysis, annotation of genetic sequences.

Features:

Integrated tools
Multiple sequence alignment using MUSCLE 3, KAlign, Clustal;
HMM profiles build and search,. Free download of Unipro UGENE 64-bit 1.11.4, size 29.57 Mb.

NCBI Genome Workbench 2.5.0 Genome Workbench Development Team 

NCBI Genome Workbench is a handy, easy to use, integrated software specially designed to help you view and analyze sequence data.

With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.

Genome Workbench can display sequence data in many ways,. Free download of NCBI Genome Workbench 2.5.0, size 0 b.

The Family Tree of Family 10.0 Perun, Ltd 

The program is designed to preserve the history and construction of a family tree of the family. With its help you create the detailed list of family members add their biographies, photos and video. The program is simple and easy to learn, has a clear and beautiful interface.
Features:
- Preparation of the biography of each family. Free download of The Family Tree of Family 10.0, size 7.67 Mb.

3D Viewer for Phylogenetic Trees 1.0 Phy3d 

A 3D viewer for phylogenetic trees. Speciation events are displayed in the plane according to the species tree, while duplication events are displayed in the other dimension.. Freeware download of 3D Viewer for Phylogenetic Trees 1.0, size 0 b.


Phylogenetic Tree Construction Web Results

Tree of Life

Phylogenetic tree with information about the diversity of organisms on Earth, their history, and characteristics. An on-going multi-authored project hosted by the University of Arizona.

Mammaliaformes- phylogenetic tree

This is Mikko Haaramo's private archive of various phylogenetic trees, starting at Mammaliaformes.

Mobile Group II Introns

Phylogenetic tree, secondary and ORF structure to identify and catalog group II introns in bacteria and other organisms, maintained by the Zimmerly Laboratory at the University of Calgary, Canada.

TreeTop

Multiple sequence alignment based phylogenetic tree prediction program.

Czech-Genealogy

Investigations undertaken by Barbora Stastna and Ladislav Urban. Includes archive search, tree construction, living relatives, and translations.

Yes Family Tree

A family tree for the various incarnations of Yes and the other bands Yes members have been part of.

Tree for Happy Holidays

ASCII Christmas tree available all year around. Made with many languages.