sequence assembly
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scf trace assembly
DNA contig assembly


An affordable alternative to the really expensive software for DNA sequence assembly and contig editing.

sequence assembling software


Molecular biology tools


sequence assembly DNA Baser Sequence Assembler  

DNA Baser Sequence Assembler is unique and revolutionary bioinformatics software for

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DNA Baser console Grid cell counter Grid cell counter Grid cell counter

This is a the command line version of DNA Baser Sequence Assembler. Now you can harness the power and accuracy of DNA Baser at a new level by performing custom sequence assembly from your own home-made (DOS) scripts.




Date of release: Aug 2011

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BaserConsole.exe ^
   /InputFolder="c:\samples\" ^
   /FileType='*.scf' ^
   /OutputFolder="c:\samples\out" ^

pause > nul

sequence assembler

FASTA to multi-FASTA

SFF Workbench 


SFF Workbench is an easy to use SFF file viewer, editor and converter. It is the first and only SFF editor with graphic interface on the entire bioinformatics market! Features:

  • Delete samples
  • Convert SFF to multiFASTA format
  • Cut a SFF file in smaller pieces
  • Sort samples by name, average quality and length
  • Append Roche index to unindexed files
  • Displays SFF file size, content, number of samples/reads, Roche details (index, manifest), average quality of each sample, sample length, mini-chromatograms, low quality (clipped) ends
  • Blazing fast, compact and portable (no installation required)
  • User-friendly graphic interface

Size: 1.3 MB

sequence assembler

Chromatogram Explorer Chromatogram Explorer  

Windows Explorer clone for DNA sequence analysis. Features:

  • Display sample's content as you browse through your folders
  • Highlight low quality regions
  • Manually or automatically trim low quality ends (batch)
  • Convert between miscellaneous formats
  • View FASTA, SEQ, TXT, SCF, ABI, AB, AB!, AB1 samples
  • View sample properties & statistics
  • Display confidence scores
  • Extract bases from chromatograms (copy to clipboard)

Size: 1 MB

Freeware - Download page

Chromatogram Explorer

sequence assembly PolyPro - Polynucleotide probe design Freeware

In situ hybridization of genes and mRNA is most often based on polynucleotide probes.

We recently developed a concept and software (PolyPro) for rational design of polynucleotide probe mixes to identify particular genes in defined taxa. PolyPro consists of three modules: a GenBank Taxonomy Extractor (GTE), a Polynucleotide Probe Designer (PPD) and a Hybridization Parameters Calculator (HPC).





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onvertrix - A Batch DNA Sample Converter

Convertrix - A Batch DNA Sample Converter  

Convertrix is a molecular biology command line tool for converting between several popular DNA sample formats. It can automatically trim the untrusted regions (low quality bases) at the end of samples. The program needs no manual: a graphic interface is available to help you to generate the command line.


Date of release: April 2010



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onvertrix - A Batch DNA Sample Converter

multi-FASTA to FASTA Everything to FASTA converter  

Everything to Fasta Converter converts the specified samples (SCF, ABI, FASTA, multiFasta, GBK, multiGBK, SEQ, TXT) to FASTA format. Starting with version 3.0 protein FASTA files are also supported.



Freeware - Details

multi-FASTA to FASTA converter

Sequence dereplicator-Free download Sequence dereplicator  

Clone Library Dereplicator simplifies the dereplication of all type sequence libraries (16S rRNA, 18S rRNA, 23S rRNA, 28S rRNA, functional and structural proteins) and prepares the raw sequences for subsequent analyses or contig assembly. Clone Library Dereplicator sorts all unique DNA sequences (FASTA) belonging to your clone libraries, by moving/coping them into the specified folder.


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Sequence dereplicator

sequence assembler

GBK to FASTA converter freeware GBK to FASTA converter  


GenBank to FASTA converter is a a freeware molecular biology tool that can convert GenBank (gb/gbk) file format to FASTA format. The converter is really small and portable. All operating systems from Windows 95 to Windows Vista.


How to use it: Locate the GBK files you want to convert and press the CONVERT button. A folder called 'Converted files' will be automatically created to store the new generated FASTA files.


Freeware - Details

GBK to FASTA converter

DNA Counter Cell counter  

Cell Counter is a freeware tool that will help you to manually count the cells shown on computer screen by displaying a transparent or semi-transparent grid over your image.


How to use it:

Open the image that contains the cells to be counted in your preferred software/image viewer. Start Grid Cell Counter, and choose the size of the grid.


Freeware - Download page

Grid cell counter

DNA Counter DNA Nucleotide Counter  

DNA Nucleotide Counter is a freeware tool that shows the proportions between nucleotides (A, C, G, T, CG, AT) in a DNA sequence.

Compact and easy to use.


Freeware - Download page

DNA Nucleotide Counter

RNA Baser Assembler RNA Baser Sequence Assembler  

RNA Baser represents an extension of DNA Baser, specialized in processing rRNA sequences. It is optimized for early integration of sequence and metadata. This way, the metadata will stay attached to the primary sequence information throughout the complete workflow of sequence analysis, until final submission. In addition, it is optimized for data exchange with standard non-commercial software used for rRNA sequence analysis and submission.


RNA Baser is a joint project of Heracle BioSoft, Ribocon GmbH and Max Planck Institute for Marine Microbiology in Bremen, Germany

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Installs in any computer!


Our bioinformatics software tools can be installed in any Windows computer and it works properly EVEN IF YOU DON'T HAVE ADMINISTRATOR RIGHTS. In this case just install the program somewhere else than Program Files; for example in a folder where you have write permissions such as 'c:\MyPersonalFolder', 'Desktop' or 'My Documents'.





Our software tools are really small so you can easily copy them on a floppy disk or USB flash stick and take them with you or send them to your colleagues via email.



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contig assembly software
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