File type	Suffix	File format used for
ACE files	.ace	contigs (only import)
Phylip Alignment	.phy	alignments
GCG Alignment	.msf	alignments
Clustal Alignment	.aln	alignments
Newick	.nwk	trees
FASTA	.fsa/.fasta	sequences
GenBank	.gbk/.gb/.gp	sequences
GCG sequence	.gcg	sequences (only import)
PIR (NBRF)	.pir	sequences (only import)
Staden	.sdn	sequences (only import)
DNAstrider	.str/.strider	sequences
Swiss-Prot	.swp	protein sequences
Lasergene sequence	.pro	protein sequence (only import)
Lasergene sequence	.seq	nucleotide sequence (only import)
Embl	.embl	nucleotide sequences
Nexus	.nxs/.nexus	sequences, trees, alignments, and sequence lists
CLC	.clc	sequences, trees, alignments, reports, etc.
Text	.txt	all data in a textual format
CSV	.csv	tables, each cell separated with semicolons (only export)
ABI	.abi	trace files (only import)
AB1	.ab1	trace files (only import)
SCF2	.scf	trace files (only import)
SCF3	.scf	trace files (only import)
Phred	.phd	trace files (only import)
mmCIF	.cif	structure (only import)
PDB	.pdb	structure (only import)
BLAST Database	.phr/.nhr	BLAST database (import)
Vector NTi Database		sequences (import of whole database)
VectorNTI achieves	.ma4/.pa4/.oa4	sequences (only import)
Gene Construction Kit	.gcc	sequences (only import)
RNA Structure	.ct/.col/.rnaml/.xml	RNA structures
Preferences	.cpf	CLC preferences

Note! CLC Genomics Workbench can import 'external' files, too. This means that all kinds of files can be imported and displayed in the Navigation Area, but the above mentioned formats are the only ones whose contents can be shown in CLC Genomics Workbench.