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Phylogentic Analysis Software

PHYLIP: PHYLIP (the Phylogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). It is available free over the Internet, and written to work on as many different kinds of computer systems as possible. The source code is distributed (in C), and executables are also distributed. In particular, already-compiled executables are available for Windows (95/98/NT/2000/me/xp/Vista), Mac OS X, Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters. PHYLIP is probably the most widely-distributed phylogeny package. It is the third most frequently cited phylogeny package, after PAUP* and MrBayes, and ahead of MEGA. PHYLIP has been in distribution since October, 1980, and has over 26,000 registered users.

MEGA: Molecular Evolutionary Genetics Analysis MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.


ptr Real-Time Caption Expert Engine

A unique facility to generate detailed captions for different types of analyses and results. These captions are intended to provide detailed, natural language descriptions of the methods and models used in analysis. The facility aims to promote a better understanding of the underlying assumptions used in analysis, and also of the results generated.

ptr Maximum Composite Likelihood Method

A method for estimating evolutionary distances between all pair of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This method can also be used to estimate transition/transversion biases and nucleotide substitution patterns without requiring a priori knowledge of the phylogenetic tree.

ptr Linux Version

This software package is now programmed to run efficiently in the Linux desktop environment on top of Wine, an open-source compatibility layer for running Windows programs on Unix-based Operating Systems.

ptr Multi-User and Multi-Threading Support

The multi-user environment will support each user of the same computer to preserve their customized settings, choice of genetic code table, and a variety of analysis options.

PAUP*: Phylogenetic Analysis Using Parsimony

PAUP* version 4.0 is a major upgrade and new release of the software package for inference of evolutionary trees, for use in Macintosh, Windows, UNIX/VMS, or DOS-based formats. The influence of high-speed computer analysis of molecular, morphological and/or behavioral data to infer phylogenetic relationships has expanded well beyond its central role in evolutionary biology, now encompassing applications in areas as diverse as conservation biology, ecology, and forensic studies. The success of previous versions of PAUP: Phylogenetic Analysis Using Parsimony has made it the most widely used software package for the inference of evolutionary trees. In addition, the PAUP manual has proven to be an essential guide, serving as a comprehensive introduction to phylogenetic analysis for beginning researchers, as well as an important reference for experts in the field. With the inclusion of maximum likelihood and distance methods in PAUP* 4.0, the new version represents a great improvement over its predecessors. In addition, the speed of the branch-and-bound algorithm has been enhanced and a number of new features have been added, from agreement subtrees to tests for combinability of data and permutation tests for nonrandomness of data structure. These, along with many other improvements, will make PAUP* 4.0 an even more indispensable tool in comparative biological analysis than were previous editions of the program and manual. PAUP* 4.0 and MacClade 3 use a common data file format (NEXUS), allowing easy interchange of data between the two programs.

EvolveAGene 3: DNA coding sequence evolution simulation program.

EvolveAGene 3 is a realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions, including variable regions of selection intensity within the sequence and variation in intensity of selection over branches. Variation includes base substitutions, insertions and deletions. Output includes a log file, the true tree and both unaligned coding sequence and protein sequences and the true DNA and protein alignments.

CompTrees 4:

Compares phylogenetic trees with each other and measures their similarity in topology and branch lengths


Aligns DNA coding sequences according to an existing alignment of the corresponding protein sequences by introducing triplet gaps into the DNA sequence at positions of gaps in the protein alignment. Phylogenies based on CodonsAligned DNA sequenecs are more accurate than are phylogenies based on dirrectly aligned DNA coding sequences.

Clustal w:

Multiple Sequence Alignment Program.

Clustal W is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Clad grams or Phylograms.

The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down weight near-duplicate sequences and upweight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.

Clustal X:

Clustal X is a new windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated allowing you to highlight conserved features in the alignment. The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment.

You can cut-and-paste sequences to change the order of the alignment; you can select a subset of sequences to be aligned; you can select a sub-range of the alignment to be realigned and inserted back into the original alignment.

Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted.

ClustalX is available for a number of different platforms including: SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECStations, Microsoft Windows (32 bit) for PC's, Linux ELF for x86 PC's and Macintosh PowerMac. (See the README file for Installation instructions.)


Is a utility that facilitates judging the quality of alignments constructed by ClustalX and aids in refining those alignments by adjusting gap penalties.

TuneClustalX reads that file and calculates an average Q-score, making it easy to know if a modification of gap penalties has improved the alignment.

Alignments can often be improved by using different gap penalties for a selected portion of the alignment. ClustalX allows you select a range of residues and apply a set of gap penalties only to that range. The effectiveness of that change can be determined by TuneClustalX by using the option to report the average Q-score for only that selected range.

T Coffee:

T-Coffee is a multiple sequence alignment program.

The main characteristic of T-Coffee is that it will allow you to combine results obtained with several alignment methods. By default, T-Coffee will compare all you sequences two by two, producing a global alignment and a series of local alignments (using lalign). The program will then combine all these alignments into a multiple alignment.