| CLC Gene Workbench
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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: CLC bio
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| CLC Protein Workbench
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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 |
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Web Site: CLC bio
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| CLC RNA Workbench
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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. |
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Web Site: www.clcbio.com
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| CONFAC
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Internet Browser |
| CONFAC identifies significantly enriched and evolutionarily conserved transcription factor binding sites (TFBS) quickly for sets of hundreds of genes found to be co-expressed by microarray analysis. |
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Web Site: CONFAC
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| Chromatogram Explorer-Exploring and trimming your chromatograms is not a problem anymore
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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. |
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Web Site: DNA Baser - Free biology software
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| Cleaner
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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. |
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Web Site: JustBio.com
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| CluClean (ClustalW Cleaner)
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Windows |
| CLUCLEAN makes the CLUSTALW output more readable. You can select a reference sequence and view the homology between the selected sequence and the other sequences. CLUCLEAN replaces the bases that are identical to the selected sequence by a dot. CLUCLEAN can also calculate a consensus sequence based on the user-defined homology percent. |
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Web Site: Olivier Friard
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| Clustal
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MS-DOS Mac Unix VMS Windows |
| ClustalW is a popular multiple sequence alignment program available for a wide range of platforms. |
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Web Site: ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/
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| ClustalW (EBI)
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Internet Browser |
| Multiple alignment of protein or DNA sequences using ClustalW algorithm. |
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Web Site: EBI
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| ClustalW (PBIL)
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Internet Browser |
| Alignment of multiple sequences using the ClustalW algorithm. |
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Web Site: PBIL
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| ClustalW 1.74 (MS-DOS)
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MS-DOS |
| Performs the multiple alignment of protein or DNA sequences. |
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Web Site: La Bioinformatique à l'IGBMC
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Download (309 kb, 16-Jan-1998) |
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| ClustalW 1.74 (Mac)
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Mac |
| Performs the multiple alignment of protein or DNA sequences. |
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Web Site: La Bioinformatique à l'IGBMC
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Download (613 kb, 16-Jan-1998) |
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| ClustalW 1.74 (Unix)
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Unix |
| Performs the multiple alignment of protein or DNA sequences. |
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Web Site: La Bioinformatique à l'IGBMC
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Download (592 kb, 17-Jan-1998) |
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| ClustalX 1.8 (Alpha)
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Unix |
| Clustal X is a general purpose multiple alignment program for DNA or proteins, using a window interface for sequence input and display. Compiled for DEC Alpha. |
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Web Site: La Bioinformatique à l'IGBMC
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Download (1180 kb, 01-Jul-1999) |
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| ClustalX 1.8 (Iris)
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Unix |
| Clustal X is a general purpose multiple alignment program for DNA or proteins, using a window interface for sequence input and display. Compiled for IRIX5.3 on Silicon Graphics. |
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Web Site: La Bioinformatique à l'IGBMC
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Download (1311 kb, 01-Jul-1999) |
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| ClustalX 1.8 (Linux)
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Linux |
| Clustal X is a general purpose multiple alignment program for DNA or proteins, using a window interface for sequence input and display. For Linux. |
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Web Site: La Bioinformatique à l'IGBMC
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Download (2743 kb, 01-Jul-1999) |
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| ClustalX 1.8 (Mac)
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Mac |
| Clustal X is a general purpose multiple alignment program for DNA or proteins, using a window interface for sequence input and display. PPC version only. |
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Web Site: La Bioinformatique à l'IGBMC
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Download (1207 kb, 01-Jul-1999) |
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| ClustalX 1.8 (Solaris)
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Unix |
| Clustal X is a general purpose multiple alignment program for DNA or proteins, using a window interface for sequence input and display. Compiled for Sun Solaris. |
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Web Site: La Bioinformatique à l'IGBMC
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Download (1275 kb, 01-Jul-1999) |
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| ClustalX 1.8 (Windows)
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Windows |
| Clustal X is a general purpose multiple alignment program for DNA or proteins, using a window interface for sequence input and display. For Windows 3.1/95/98/NT. |
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Web Site: La Bioinformatique à l'IGBMC
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Download (440 kb, 01-Jul-1999) |
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| CodonCode Aligner Sequence Assembler
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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. |
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Web Site: CodonCode Aligner Sequence Assembly and Alignment
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| CompLib 2.0
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Unix |
| Complib is a general platform for sequence comparison programs that compares one library of sequences - the query library - against a (typically) much larger library of sequences, such as Swiss-Prot or PIR (for proteins) of Genbank. This file contains source code for the pvm3 version of CompLib. |
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Download (64 kb, 24-Feb-1994) |
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| Consense 1.1
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MS-DOS |
| A program to calculate consensus sequences from alignments, which allows identification of protein domains and improvement of alignments. |
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Download (35 kb, 21-Jun-1993) |
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| Convers Manual
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Unix |
| Instructions for Convers (program included with DSCE package). |
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Download (23 kb, 04-Jan-1995) |
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| Covariation
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Mac |
| Identification of compensating base changes and covariations in aligned RNA sequences. |
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Download (115 kb, 30-Jul-1991) |
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| DCSE
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Unix |
| DCSE (Dedicated Comparative Sequence Editor) provides a user-friendly, menu-driven environment to make and maintain sequence alignments. It can be used to edit protein, DNA or RNA alignments. The structure of the molecules can be incorporated in the alignment. |
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Download (3304 kb, 04-Jan-1995) |
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