| ABLE | CAIC | COMPONENT |
| COMPROB | ClustalW | GDE |
| Hennig86 | MALIGN | MARKOV |
| MEGA | MOLPHY | MUST |
| MacClade | MacT | Molevol |
| ODEN | PAML | PARBOOT |
| PAUP | RSVP | SINCAIDEN |
| TreeAlign | TreeTool | WINCLADA |
Analysis of Branch Length Errors. ABLE is a package of three programs which allows you to perform a test for constancy of evolutionary rates, as proposed by Adell and Dopazo (J. Mol. Evol. 38:305-309.). The idea of the test is to simulate a large number of evolutionary processes corresponding to the proposed model and then construct the statistical distribution of the branch lengths. A tree is then reconstructed without the constraints imposed by the model and that tree is checked against expectations. It is designed for use with Phylip, and requires at least the FITCH and KITSCH programs. ABLE runs on PCs, and is available at no cost.
Comparative Analysis of Indepenent Contrasts. CAIC is a Macintosh program, which uses the contrast method, as described in the article by Purvis and Rambaut (CABIOS 11:247-251.). It is available at no charge.
CLadistic INference by Compatibility of Hypothesized CHaracters. The original DOS program for cladistic compatibility analysis. Includes Fortran source. Available at no cost.
COMPONENT is a windows program for analysing evolutionary trees. It is intended for use in studies of phylogeny, tree shape distribution, gene trees/species trees, host-parasite cospeciation, and biogeography. It has a user-friendly interface, supports standard tree files (NEXUS, Hennig86, PHYLIP), and has several nice features. It costs 40 pounds, and ordering details can be found on its site.
COMPROB is a Pascal program which calculates the probability that any two characters would be compatible. It is free, and can be obtained by email from its creator at meacham@violet.berkeley.edu.
ClustalW is the lastest of the Clustal programs, which are a series of programs for multisequence alignment that estimate trees as they aling multiple sequences. It is available for most archetechures, can read several input formats, and is described in two papers. It is available free of charge.
Generic Data Environment. GDE is an interactive sequence editor which allows the user to edit sequences and align them by hand. It can invoke several programs, inlucluding ClustalV, several of the Phylip 3.5 programs and the TreeTool plotting program. It is available for free.
Hennig86 is a fast parsimony program which includes branch and bound search and interactive rearangement. It costs $50, plus five for shipping.
MALIGN is a parsimony-based alignment method for sequences. It finds the phylogeny and alignment at the same time by minimizing the scores along the tree. It is described in Cladistics 12:1-9. It runs on either Unix or Dos, and is available free.
MARKOV computes a distance measure between pairs of sequences. It constructs phylogenies from these and summarizes the 4x4 substitution matrices between species. Its sustitution method is described in a paper by Saccone et. al. in Methods of Enzymology 183:570-583. It runs on UNIX or VMS, and can be obtained by email from lanave@vaxba0.ba.it.
Molecular Evolutionary Genetic Analysis. MEGA is a general purpose package, providing several different methods for tree construction, including various parsimony algorithms and the neighbor joining method. It also does distance estimation. The program runs under PC operating systems, and costs $15.
MOLPHY stands for Molecular Phylogeny. It is a package consisting of several C and Perl utilities which calculate phylogeny using maximum likelihood and neighbor joining methods. It runs under UNIX and is available for free.
MUST is a package of sequence management programs. It is intended for use with existing phylogeny programs and can produce output in Phylip, PAUP, Hennig86, and CLUSTAL formats. It runs under DOS. It is available free if you mail diskettes to the author, or as shareware otherwise. For more information, email hp@bio4.bc4.u-psud.fr.
MacClade provides tools for the graphic and interactive analysis of phylogeny and character evolution. The program includes many tools for data manipulation, including molecular sequence alignment. It runs under MacOS, and costs $125.
MacT computes distances and neighbor-joining phylogenies. It works on four to twenty-six sequences. MacT runs under MacOS, and is available at no cost.
Molevol is a set of several programs which allow you to estimate trees by parsimony or distance methods. It also includes programs to manipulate the data and search for secondary structure. The package runs under DOS, and is available for free. For more information, email wfitch@daedalus.bio.uci.edu.
NJPlot is a program which plots phylogenic trees and saves them as Postscript. It is available free for a variety of archetectures.
ODEN is a package which performs distance matrix analysis on sequences. It is desribed in CABIOS 10: 11-12. It is available for free.
PAML is a package for doing maximum likelihood analysis on sequences. It can estimate branch lengths in phylogenic trees and various evolutionary values. It can also test evolutionary models and simulate sequence evolution, and it can build trees. It runs under Unix, Windows, and Mac, and is freely available.
PARBOOT takes bootstrap sampled data sets and splits them up, sending each to a different machine, to speed up the process. It requires both Phylip and Perl, and is available at no cost.
PAUP originally stood for Phylogenic Analysis Using Parsimony, but has become one of the major software packages for phylogenic work. It includes parsimony, maximum likelihood, and distance techniques. It also has several statistical tests included. It is available for many archetectures, but costs around $100, depending on version and license.
Restriction Site Variability Program. RSVP calculates several measures of genetic variability based on restriction map data. It also produces distance matrices from collections of restriction maps. It runs under Unix and is available free.
SINCAIDEN is sold as a workstation with program which allows researches to easily generate phylogenic trees. It also allows searches of the major sequence databases. There are several methods available. This system costs $28,000.
TreeAlign is a multiple sequence alignment program that builds trees as it aligns sequences. It use a blend of distance matrices and parsimony. It is designed for use on a workstation or mainframe. It is freely available.
TreeTool is an interactive tool for displaying, editing and printing phylogenic trees. It runs under Unix, and is free.
Winclada is an interactive program which allows the user to display, manipulate, and print phylogenic trees. It has various tree operations and can read several types of input file. It is available as shareware, and costs $50 to register.