Comparison of workbenches

Below we list a number of functionalities that differ between CLC Workbenches and the CLC Sequence Viewer:

 Data handling Viewer Main Genomics      
 Add multiple locations to Navigation Area   Image combined Image genomics      
 Share data on network drive   Image combined Image genomics      
 Search all your data   Image combined Image genomics      

 Assembly of sequencing data Viewer Main Genomics      
 Advanced contig assembly   Image combined Image genomics      
 Importing and viewing trace data   Image combined Image genomics      
 Trim sequences   Image combined Image genomics      
 Assemble without use of reference sequence   Image combined Image genomics      
 Map to reference sequence   Image combined Image genomics      
 Assemble to existing contig   Image combined Image genomics      
 Viewing and edit contigs   Image combined Image genomics      
 Tabular view of an assembled contig (easy data overview)   Image combined Image genomics      
 Secondary peak calling   Image combined Image genomics      
 Multiplexing based on barcode or name   Image combined Image genomics      

 Next-generation Sequencing Data Analysis Viewer Main Genomics      
 Import of 454, Illumina Genome Analyzer, SOLiD and Helicos data     Image genomics      
 Reference assembly of human-size genomes     Image genomics      
 De novo assembly     Image genomics      
 SNP/DIP detection     Image genomics      
 Graphical display of large contigs     Image genomics      
 Support for mixed-data assembly     Image genomics      
 Paired data support     Image genomics      
 RNA-Seq analysis     Image genomics      
 Expression profiling by tags     Image genomics      
 ChIP-Seq analysis     Image genomics      

 Expression Analysis Viewer Main Genomics      
 Import of Illumina BeadChip, Affymetrix, GEO data   Image combined Image genomics      
 Import of Gene Ontology annotation files   Image combined Image genomics      
 Import of Custom expression data table and Custom annotation files   Image combined Image genomics      
 Multigroup comparisons   Image combined Image genomics      
 Advanced plots: scatter plot, volcano plot, box plot and MA plot   Image combined Image genomics      
 Hierarchical clustering   Image combined Image genomics      
 Statistical analysis on count-based and gaussian data   Image combined Image genomics      
 Annotation tests   Image combined Image genomics      
 Principal component analysis (PCA)   Image combined Image genomics      
 Hierarchical clustering and heat maps   Image combined Image genomics      
 Analysis of RNA-Seq/Tag profiling samples   Image combined Image genomics      

 Molecular cloning Viewer Main Genomics      
 Advanced molecular cloning   Image combined Image genomics      
 Graphical display of in silico cloning   Image combined Image genomics      
 Advanced sequence manipulation   Image combined Image genomics      

 Database searches Viewer Main Genomics      
 GenBank Entrez searches Image free Image combined Image genomics      
 UniProt searches (Swiss-Prot/TrEMBL)   Image combined Image genomics      
 Web-based sequence search using BLAST   Image combined Image genomics      
 BLAST on local database   Image combined Image genomics      
 Creation of local BLAST database   Image combined Image genomics      
 PubMed lookup   Image combined Image genomics      
 Web-based lookup of sequence data   Image combined Image genomics      
 Search for structures (at NCBI)   Image combined Image genomics      

 General sequence analyses Viewer Main Genomics      
 Linear sequence view Image free Image combined Image genomics      
 Circular sequence view Image free Image combined Image genomics      
 Text based sequence view   Image combined Image genomics      
 Editing sequences Image free Image combined Image genomics      
 Adding and editing sequence annotations   Image combined Image genomics      
 Advanced annotation table   Image combined Image genomics      
 Join multiple sequences into one Image free Image combined Image genomics      
 Sequence statistics Image free Image combined Image genomics      
 Shuffle sequence Image free Image combined Image genomics      
 Local complexity region analyses   Image combined Image genomics      
 Advanced protein statistics   Image combined Image genomics      
 Comprehensive protein characteristics report   Image combined Image genomics      

 Nucleotide analyses Viewer Main Genomics      
 Basic gene finding Image free Image combined Image genomics      
 Reverse complement without loss of annotation Image free Image combined Image genomics      
 Restriction site analysis Image free Image combined Image genomics      
 Advanced interactive restriction site analysis   Image combined Image genomics      
 Translation of sequences from DNA to proteins Image free Image combined Image genomics      
 Interactive translations of sequences and alignments   Image combined Image genomics      
 G/C content analyses and graphs   Image combined Image genomics      

 Protein analyses Viewer Main Genomics      
 3D molecule view   Image combined Image genomics      
 Hydrophobicity analyses   Image combined Image genomics      
 Antigenicity analysis   Image combined Image genomics      
 Protein charge analysis   Image combined Image genomics      
 Reverse translation from protein to DNA   Image combined Image genomics      
 Proteolytic cleavage detection   Image combined Image genomics      
 Prediction of signal peptides (SignalP)   Image combined Image genomics      
 Transmembrane helix prediction (TMHMM)   Image combined Image genomics      
 Secondary protein structure prediction   Image combined Image genomics      
 PFAM domain search   Image combined Image genomics      

 Sequence alignment Viewer Main Genomics      
 Multiple sequence alignments (Two algorithms) Image free Image combined Image genomics      
 Advanced re-alignment and fix-point alignment options   Image combined Image genomics      
 Advanced alignment editing options Image free Image combined Image genomics      
 Join multiple alignments into one   Image combined Image genomics      
 Consensus sequence determination and management Image free Image combined Image genomics      
 Conservation score along sequences Image free Image combined Image genomics      
 Sequence logo graphs along alignments   Image combined Image genomics      
 Gap fraction graphs   Image combined Image genomics      
 Copy annotations between sequences in alignments   Image combined Image genomics      
 Pairwise comparison Image free Image combined Image genomics      

 RNA secondary structure Viewer Main Genomics      
 Advanced prediction of RNA secondary structure   Image combined Image genomics      
 Integrated use of base pairing constraints   Image combined Image genomics      
 Graphical view and editing of secondary structure   Image combined Image genomics      
 Info about energy contributions of structure elements   Image combined Image genomics      
 Prediction of multiple sub-optimal structures   Image combined Image genomics      
 Evaluate structure hypothesis   Image combined Image genomics      
 Structure scanning   Image combined Image genomics      
 Partition function   Image combined Image genomics      

 Dot plots Viewer Main Genomics      
 Dot plot based analyses   Image combined Image genomics      

 Phylogenetic trees Viewer Main Genomics      
 Neighbor-joining and UPGMA phylogenies Image free Image combined Image genomics      
 Maximum likelihood phylogeny of nucleotides   Image combined Image genomics      

 Pattern discovery Viewer Main Genomics      
 Search for sequence match Image free Image combined Image genomics      
 Motif search for basic patterns   Image combined Image genomics      
 Motif search with regular expressions   Image combined Image genomics      
 Motif search with ProSite patterns   Image combined Image genomics      
 Pattern discovery   Image combined Image genomics      

 Primer design Viewer Main Genomics      
 Advanced primer design tools   Image combined Image genomics      
 Detailed primer and probe parameters   Image combined Image genomics      
 Graphical display of primers   Image combined Image genomics      
 Generation of primer design output   Image combined Image genomics      
 Support for Standard PCR   Image combined Image genomics      
 Support for Nested PCR   Image combined Image genomics      
 Support for TaqMan PCR   Image combined Image genomics      
 Support for Sequencing primers   Image combined Image genomics      
 Alignment based primer design   Image combined Image genomics      
 Alignment based TaqMan probe design   Image combined Image genomics      
 Match primer with sequence   Image combined Image genomics      
 Ordering of primers   Image combined Image genomics      
 Advanced analysis of primer properties   Image combined Image genomics      

 Molecular cloning Viewer Main Genomics      
 Advanced molecular cloning   Image combined Image genomics      
 Graphical display of in silico cloning   Image combined Image genomics      
 Advanced sequence manipulation   Image combined Image genomics      

 Virtual gel view Viewer Main Genomics      
 Fully integrated virtual 1D DNA gel simulator   Image combined Image genomics