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	Data structure and data sharing
	All types of files can be saved in local projects
	Full support for CLC Bioinformatics Database

Printing and reporting

	Printing of reports and graphics
	User-designed graphics output

Import and export

	Export of user-defined figures to various graphics file formats
	Import and export of data in a wide range of file formats

History

	Detailed history log

Batch processing

	Processing of multiple analyses in one single work-step

Customize solutions

	Full customization of your workbenches

Next Gen. Sequencing

Genomics

	de novo assembly of mixed datasets
	Contig report
	Reference assembly of mixed datasets
	Detection of large scale mutations and rearrangements
	Masking of reference assembly based on annotation like e.g. exons
	Interactive and zoom-able viewing of genome assemblies
	Advanced SNP detection, including choice of ploidity
	SNP reporting
	Advanced DIP detection, including choice of ploidity
	DIP reporting

Transcriptomics

	Support for micro-array based expression data.
	Support for sequencing based (RNA-seq) expression data
	Calculation of gene expression measures (RPKM)
	Advanced RNA-seqoutputs comparing expression levels of count-based expresssion measures
	Discovery of novel transcripts/exons
	Interactive views of assemblies and derived gene expression data
	Visualization: Interactive heat map, table and scatter plot views
	Transformation and normalization tools
	Quality control tools
	Two- or multiple group comparisons
	Multiple testing corrected p-values (Bonferroni and/or FDR)
	Several clustering algorithms
	Ability to import NetAffx, Illumina annotation arrays and adding annotation to experiments
	Tools for Gene Set Enrichment Analysis (GSEA) and for Hyper-Geometric based tests for overrepresented annotation categories (e.g. 'GO'stats or specific protein pathways)
	Facility for annotating sequences from GFF or GTF files

Epigenomics

	Chromatin immunoprecipitation sequencing analysis
	Peak finding and peak refinement
	Graph and table of background distribution and false discovery rate
	Peak table and annotations

General NGS features

	Support for multiplex sequencing by file name
	Support for multiplex sequencing by sample-specific tag
	Quality reporting and statistics on raw data

Other Bioinformatics features

RNA secondary structure

	Secondary structure prediction
	Advanced options
	Graphical view and editing of secondary structure
	Tabular view of structures and energy contributions
	Symbolic representation in sequence view

BLAST searches

	BLAST searches
	Create local BLAST databases
	Table view of BLAST results (easy data overview)
	BLAST against local databases
	Web-based sequence search using BLAST
	Graphical view of BLAST search
	SNP annotation using BLAST

Other database searches

	GenBank Entrez searches
	UniProt searches (Swiss-Prot/TrEMBL)
	PubMed lookup
	Web-based lookup of sequence data

Protein analyses

	Integrated 3D molecule viewer
	Simultanious view of sequences in 2D and 3D
	Hydrophobicity analyses
	Antigenicity analysis
	Protein charge analysis
	Reverse translation from protein to DNA
	Proteolytic cleavage detection
	Prediction of signal peptides (SignalP)
	Transmembrane helix prediction (TMHMM)
	Secondary protein structure prediction
	PFAM domain search

Dot plots

	Dot plot based analyses

Primer design

	Advanced and automated primer design tools
	In silico PCR
	Detailed primer and probe parameters
	Graphical display of primers
	Generation of primer design output
	Support for Standard PCR
	Support for Nested PCR
	Support for TaqMan PCR
	Support for Sequencing primers
	Alignment based primer design
	Alignment based TaqMan probedesign
	Match primer with sequence
	Ordering of primers
	Advanced analysis of primer properties

Assembly of Sanger sequencing data

	Advanced contig assembly
	Importing, viewing, and editing trace data
	Trim sequences
	Secondary peak calling
	Assemble without use of reference sequence
	Assemble to reference sequence
	Assemble to an existing contig
	Viewing contigs
	Editing contigs
	Tabular view of an assembled contig (easy data overview)

Molecular cloning

	Advanced molecular cloning
	Gateway Cloning
	Graphical display of in silico cloning
	Advanced sequence manipulation

Virtual gel viewer

	Fully integrated virtual 1D DNA gel simulator

Pattern discovery

	Search for sequence match
	Motif search for basic patterns
	Motif search with regular expressions
	Motif search with PROSITE patterns
	Pattern discovery

General sequence analyses

	Linear sequence view
	Circular sequence view
	Text based sequence view
	One-click switch between different views of a sequence
	Editing sequences
	Adding and editing sequence annotations
	Sequence statistics
	Shuffle sequence
	Local complexity region analyses
	Advanced protein statistics
	Comprehensive protein characteristics report
	Join multiple sequences into one
	Extract annotations

Nucleotide analyses

	Basic gene finding
	Reverse complement without loss of annotation
	Advanced interactive restriction site analysis
	Translation of sequences from DNA to proteins
	Interactive translations of sequences and alignments
	G/C content analyses and graphs

Sequence alignment

	Multiple sequence alignments (Two proprietary algorithms)
	ClustalW
	Muscle
	T-Coffee
	MAFFT
	Kalign
	Advanced re-alignment and fix-point alignment options
	Advanced alignment editing options
	Join multiple alignments into one
	Consensus sequence determination and management
	Conservation score along sequences
	Sequence logo graphs along DNA, RNA, and protein alignments
	Gap fraction graphs
	Copy features between sequences in alignments
	Advanced pairwise comparison

Phylogenetic trees

	Neighbor-joining and UPGMA phylogenies

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