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AMP Accepted-mutation parsimony MS-DOS  Mac  Unix
A data-set-derived amino acid substituted probability matrix to weight multiple, independently seeded, heuristic parsimony analysis. C source code is available.
Web Site Home Web Site: University Pennsylvania

Align Mac
This archive contains a series of programs for use in PROTEIN sequence alignment and phylogenetic tree construction. The logic of the method is described in the article "Progressive Sequence Alignment As A Prerequisite to Correct Phylogenetic Trees" by D. F. Feng and R. F. Doolittle in J. Mol. Evol. 25:351 (1987).
Download  (505 kb, 04-Jun-1993)

Aligner Internet Browser
With this tool you can align easily your multiple sequences DNA or protein, based on a Clustalw engine.
Web Site Home Web Site: JustBio.com

BIONJ MS-DOS  Mac  Unix
A phylogenic reconstruction algorithm, which uses an improved version of the NJ algorithm, and is well adapted when evolutionary distances are obtained from aligned sequences.
Web Site Home Web Site: Olivier Gascuel

BLOCK Linux  MS-DOS  Unix
Blocking Gibbs sampler for pedigree analysis. This program is for linkage analysis of large complex pedigrees.
Web Site Home Web Site: Aalborg University

BioEdit Windows
BioEdit is a full integrated sequence/alignment editor. Performs translations, phylogenetic analysis, clustalw alignments, ABI trace analysis, RNA comparitive analysis and BLAST searches. Freeware.
Web Site Home Web Site: Department o Microbiology, North Carolina State Unversity

BioNumerics Windows
One universal bioinformatics solution to store and analyze all your biological data. Powerful databasing, integrated networking and a wide range of analysis, visualization and decision-making tools, including data mining, querying, clustering, identification, statistics, and much more. With applications for bacteriology, virology and mycology including features for surveillance networks for bacterial (Salmonella, E. coli & Shigella, Campylobacter spp., Listeria monocytogenes, Vibrio cholerae, Vibrio parahaemolyticus, Yersinia pestis, etc.) and viral pathogens (norovirus).
Web Site Home Web Site: Applied Maths

CAFCA: Collection of APL Functions for Cladistic Analysis Mac
A program which employs the methods of group-compatibility and component-compatibility to run cladistic analysis of a data matrix.
Web Site Home Web Site: Leiden University

CAIC Mac
This software implements a suite of phylogenetically comparative methods for data sets including continuous variables.
Web Site Home Web Site: University of Oxford

CGR 1.0 Mac
Information by clustering the sequence alignments.
Download  (50 kb, 10-Aug-1990)

CLC Combined Workbench Linux  Mac  Windows
CLC Combined Workbench 1.0 aggregates all DNA sequence analyses of CLC Gene Workbench and all protein sequence analyses of CLC Protein Workbench. All analyses are fully integrated in one single, user-friendly, and intuitive software application. Some analyses are - Assembly of DNA sequencing data - Advanced primer design - Molecular cloning - Automatic SNP annotation of sequences - Secondary protein structure prediction - Signal Peptide Prediction (SignalP) - Transmembrane helix prediction (TMHMM) - Protein family analysis (PFAM) - 2 types of alignments - Phylogenetics - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Dot plots - Hydrophobicity analyses - Antigenicity analyses - Searches on GenBank, SwissProt, TrEMBL, and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

CLC Free Workbench 1.0 Linux  Mac  Windows
CLC Free Workbench creates a software environment enabling users to make basic bioinformatics analyses and smooth data management, combined with excellent graphical viewing and output options. Some bioinformatics features are: - GenBank searching and viewing (linear and circular views) - Multiple alignment of DNA, RNA and proteins (2 alignment algorithms) - Open reading frame determination - Translation from DNA to proteins (all genetic translation tables) - Reports with residue composition, molecular weight and iso electric point (for proteins) - Neighbor-joining and UPGMA phylogenies - Restriction site analysis and viewing - Other reporting facilities - Import/export to a number of data formats - Launch of external files - Detailed History Log
Web Site Home Web Site: CLC bio

CLC Gene Workbench Linux  Mac  Windows
CLC Gene Workbench 1.0 provides a wide range of advanced DNA sequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench. Some analyses are - Assembly of DNA sequencing data - Advanced primer design - Molecular cloning - Automatic SNP annotation of sequences - 2 types of alignments - Phylogenetics - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Dot plots - Hydrophobicity analyses - Searches on GenBank and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

CLC Protein Workbench Linux  Mac  Windows
CLC Protein Workbench 1.5 provides a wide range of advanced protein sequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench. Some analyses are - Advanced and integrated 3D molecular viewer - 2 types of alignments - Phylogenetics - Secondary protein structure prediction - Signal Peptide Prediction (SignalP) - Transmembrane helix prediction (TMHMM) - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Protein family analysis (PFAM) - Dot plots - Hydrophobicity analyses - Antigenicity analyses - Searches on GenBank, Swiss-Prot, TrEMBL, and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

CLC RNA Workbench Linux  Mac  Windows
CLC RNA Workbench aggregates a large number of advanced RNA sequence analyses and other bioinformatics analyses in one single, integrated, user-friendly, and intuitive software application. Some features are Secondary RNA structure prediction, Graphical view and editing of secondary RNA structures, Tabular view of RNA structures and RNA energy contributions, Symbolic representation of RNAs in sequence view, Pattern search, Search for sequence matches, Motif search for basic patterns, Motif search using regular expressions, Motif search with ProSite patterns, Pattern discovery (unknown patterns), Project and data management, Detailed history log, All types of files can be saved in local projects, and launched from the program, DNA, RNA and protein sequence editor displaying both linear and circular molecules, Multiple alignment of DNA, RNA, and proteins: ClustalW, Muscle, T-Coffee, MAFFT, Kalign. Interactive logo graphs along both DNA, RNA and Protein alignments, BLAST, and much more.
Web Site Home Web Site: www.clcbio.com

COMPARE MS-DOS  Unix  Windows
Consists of several programs which analyze comparative or interspecific data while taking phylogenetic information into account.
Web Site Home Web Site: University of Oregon

Chromatogram Explorer-Exploring and trimming your chromatograms is not a problem anymore Mac  Windows
Chromatogram Explorer is a very easy to use tool that will list all chromatogram files (SCF, ABI, AB1, AB) in the current folder. You can view the chromatograms while browsing through folders using its integrated Windows Explorer. Chromatogram Explorer can also trim low quality bases at the ends of your samples with a single push of a button! Now you can process/sort/search chromatograms in seconds.
Web Site Home Web Site: DNA Baser - Free biology software

Cleaner Internet Browser
With this tool you can simply and quickly clean your sequences from unwanted text marks and spaces. This is useful after retrieving sequences from online databases for example.
Web Site Home Web Site: JustBio.com

ClustToTree 1.0 Mac
Conversion of Clustal output to TreeDraw format.
Download  (31 kb, 27-Apr-1994)

Cluster Unix
A clustering program that uses single and complete linkage methods to determine the heirarchial clustering for a given data set. Accepts FASTA and BLAST outputs.
Web Site Home Web Site: University of Alberta Download  (1089 kb, 31-Mar-1998)

CodonCode Aligner Sequence Assembler Mac  Windows
CodonCode Aligner is user-friendly software for DNA sequence assembly and alignment. Features include end clipping, vector trimming, sequence assembly, alignment to reference sequences, cDNA to genomic DNA alignment, contig editing, and mutation detection. CodonCode Aligner offers many time saving and unique features, including the ability to align contigs with Clustal and muscle, trace sharpening, roundtrip editing, and base calling with Phred.
Web Site Home Web Site: CodonCode Aligner Sequence Assembly and Alignment

DIG - Analysis, Reporting, Intelligence Linux  Unix  Windows
DIG is a Data Analysis, Reporting, Intelligence tool for data workers, labs, and webmasters. Use DIG to clean up duplicates, consolidate, trim, query, summarize large data set in Excel/Access, log files, Oracle, MySQL, lab or POS systems, or any databases. Comes with powerful Excel/Access add-ons, ad-hoc query & multi-dimensional analysis. Watch on-line demo, get a free 30-day trial, then pay $96/yr or $8/month.
Web Site Home Web Site: DigDB

DIPLOMO MS-DOS
This program is a phylogenetic workbench.
Web Site Home Web Site: ANU's Research School of Biological Sciences

DISTREE 1.2 MS-DOS  Unix
DISTREE computes pairwise distances (substitution rates) of aligned nucleotide sequences utilizing various models of base substitutions and estimates standard errors of those distances.
Web Site Home Web Site: Technische Universität München Download  (64 kb, 15-Apr-1997)

DNA Translator and Aligner 1.0n Mac
DNA Translator and Aligner are Hypercard stacks to translate sequences and aid phylogenetic analysis of molecules
Download  (770 kb, 06-Apr-1994)

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