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.
Features:
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.
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.
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.
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
CodonAlign:
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.)
TuneClustalX:
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.
