Software

This is a list of some taxonomic and phylogenetic software, with emphasis on tree building and molecular data. There are also links to other, more extensive collections that may have what you're looking for if you can't find it here.

Contents

Tree viewing

Tree building

Tree comparison and interpretation

Sequence format converters

Sequence alignment, analysis, and searching

RNA secondary structure

Software archives


Tree viewing

TreeView

View NEXUS and PHYLIP format tree files on Macs (68K and Power Mac) and Windows (16 and 32 bit).

TreeExplorer

View and manipulate MEGA format trees under Windows.


Tree building

CAFCA

Collection of APL Functions for Cladistic Analysis, written by Rino Zandee. Currently Macintosh only, but Windows version coming.

PAUP 3.0

Standard program for phylogenetic analysis (currently Macintosh only but PAUP* for PowerMac, DOS, and Unix is coming).

PHYLIP

The most comphrehensive, all imbracing collection of phylogenetic programs, including parsimony, maximum likelihood, and distance methods, plus utility programs. Runs on anything.

U.K. mirror site for PHYLIP

Spectrum

Finds bipartition spectra of molecular data (Macintosh and Windows95/NT).

SplitsTree 2.0

Written by Daniel Huson, SplitsTree uses split decomposition to construct networks of relationship. The program supports the NEXUS file format, and runs on Apple Macintosh and Unix machines. There is also a Web version. The program can be downloaded from the SplitsTree ftp site.


Other lists of tree building programs

Tree of Life list of phylogeny programs

Joe Felsenstein's list of phylogeny software

Willi Hennig Society list


Tree comparsion and interpretation

MacClade 3.0

Interactive character analysis using parsimony. Wonderful! (Macintosh only)

CAIC

Comparative method (Macintosh only)

COMPONENT

Comphrehensive set of tree comparison, consensus, and randomisation methods (Windows only).

TreeMap

Software for comparing host and parasite phylogenies (Windows and Macintosh).

LAMARC

Programs for estimating population parameters from molecular sequence data.

U.K. mirror site for LAMARC


Sequence format converters

ForCon

ForCon is a user-friendly software tool for the conversion of nucleic acid and amino acid sequence alignments. Requires Windows.

SeqVerter

SeqVerter v. 1.4 is a free sequence file format conversion utility by GeneStudio, Inc. Requires Windows 95/NT (you may need to update your MFC librariers for this program).


Sequence alignment, analysis and searching

MACAW

Multiple sequence alignments, for both Windows (3.1, NT on Intel and Alpha chips) and Macintosh.

SeAl

Se-Al is a Macintosh application for creating multiple sequence alignments from nucleotide and amino acid sequences. At the moment it does not do any automatic alignments but is intended for the production of hand alignments and forpreparing input for alignment programs such as CLUSTAL and phylogeny reconstruction programs such as PHYLIP and PAUP. It is particularly useful for manipulating protein coding DNA/RNA sequences.

SeqApp

Multiple sequence alignments, including Blast searches and links to other applications. For Macintosh only but see SeqPup which will run on Mac's, Windows PC's and Unix.

SeqPup

Multiple sequence alignments, including Blast searches and links to other applications. Written in Java.

Mega2

Sequence and phylogentetic analysis program, now with a Windows interface. The DOS version of MEGA is still available

BioEdit

BioEdit is a graphical biological sequence alignment editor and analysis program for Windows 95. It is offered as is and free of charge to anyone who wants it. Features include manual and automated multiple sequence alignment, colored/shaded views, World Wide Web functions, BLAST accessories, and link to external analysis programs such as Clustal and TreeView. (for Windows 95/NT)

NEntrez

Interactive searching of GENBANK from your desktop via the Internet (see also NCBI's WWW version of Entrez). For Windows and Macintosh.


RNA secondary structure

LoopDLoop

A tool for drawing RNA secondary structures in molecular biology on Apple Macintosh computers.

LoopDLoop

A tool for drawing RNA secondary structures in molecular biology. Written in Java and runs on Macintosh, Windows and Unix machines.

RNADraw

Compute and display secondary structures under Windows 95/NT.

RNAStructure

Compute and display secondary structures under Windows 95/NT.

RnaViz

A tool for drawing RNA secondary structures on PC's running Windows 95/NT or Linux (requires TCL).

SStructView

A Java applet for displaying secondary structure in a Web browser.


Software Archives

DELTA

Harvey Group Home Page (CAIC and Bi-De, plus molecular evolution software for Apple Macintosh)

Macintosh Molecular Biology archive at Indiana

Molecular Evolution archive at Indiana

Tree of Life list of phylogeny programs

Joe Felsenstein's list of phylogeny software

Willi Hennig Society list




This page last updated 7 September 2000.