Quick. Simple. 

User-friendly BLAST Client

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Products Overview


Desktop App for Windows & Mac

  • Remote Blast+ search using EBI Server
  • 32-bit or 64-bit Local NCBI Blast Search
  • Unlimited multiple query sequences submission.


Desktop App for Windows & Mac

  • 64-bit Local NCBI Blast+ Search
  • Support large virtual database
  • Unlimited multiple query sequences submission.



Desktop App for Windows & Mac

  • Convert FASTQ file to FASTA file with easy-to-use Graphical User Interface.
  • Convert up to 10 MB FASTQ files for free.
  • FASTQ file size is unlimited with permanent license.


I use BlastStation2 for identifying and characterizing genes in pathogenic fungi. The user interface is very intuitive and easy to use. The data output is available in several different formats. The customer service is excellent and I have experienced no crashes.

Theo N Kirkland, MD
University of California, San Diego School of Medicine

I use BlastStation to conveniently search large RNA-seq transcriptomic data files obtained from tissues of non-model species. The software has made it a breeze to match unknown sequences to a known sequence from another species. The GUI is very user friendly and I have not experienced any problems with the software crashing. The use of BlastStation has saved me hours of time.

Jonathan A. W. Stecyk
University of Alaska Anchorage

I've used Blaststation mainly to probe RNA-Seq data, but also used it to search genome sequence data. I find it very convenient to be able to quickly create a database from a large transcriptome fasta file or a genome sequence file, which can then be used to blast against with either a single sequence or a fasta file of multiple sequences. The graphic output is also visually helpful.

Sibel I. Karchner
Woods Hole Oceanographic Institution

My laboratory builds genealogical trees based on analysis of DNA sequences to conduct research on evolution. When we gather new DNA sequences, it is necessary for us to make a quick comparison to known sequences. BlastStation makes this process and displays results in a clear visual interface. In addition, the staff responded to my questions and requests promptly and extremely thoroughly. I look forward to continuing to use this user friendly tool as an integral part of my laboratory.

Yoshinori Kumazawa
Nagoya City University

Our Users

Our users spread across more than 30 countries in seven continents



1. What is BlastStation?
BlastStation is a tool that speeds up BLAST homology searches and identifies DNA or proteins in the database that have similar sequences. Currently, BlastStation2 supports searches using the EBI server and local NCBI BLAST searches on your PC.  
All searches are conducted in the same easy to use interface.

2. What are the differences between different BlastStations products?
BlastStation2 is the flagship BlastStation that allows you to perform NCBI BLAST searches using the EBI server and local NCBI searches on your PC.

BlastStation-Local64 is specialized to 64-bit local NCBI BLAST+ searches.

BlastStation-Workgroup is a web-based local BlastStation designed for small to mid sized groups.

3. How many query sequences can I submit in one job?
There is no limit to the number of query sequences you can submit in production versions. For example, one of our customers performed a local BLAST search with 49,000 query sequences.
However, for our trial versions, query sequences are limited to 100 for BlastStation-Local64 and 150 for BlastStation2.

4. Why do I receive the error message “We have not received your payment”when I launch the program even though I’ve purchased the BlastStation license?
The BlastStation license is only valid for one machine. This means that your license is only valid on one PC. When you attempt to use the same license on more than one PC, this error message will show. If you would like to transfer your license to another PC, please submit a license transfer request here. We accept license transfer requests at most once every 6 months.

If you do not see your question above, please contact us here and we’d be happy to help.


TM Software, Inc.

PMB 282, 713 W. Duarte Rd., #G
Arcadia, CA 91007, USA