sequence assembly
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scf trace assembly
DNA contig assembly

DNA Sequence Assembler

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Affordable DNA sequence assembly, sequence alignment and contig editing

sequence assembling software

Program description


DNA Sequence Assembler is easy to use software for DNA sequence assembly/alignment, DNA sequence analysis, DNA Sequence manipulation and conversion, contig editing and mutation detection.


Instant download


DNA Baser Sequence Assembler

Sequence assembly software

Release date
Package size
~15 MB
Download time 5 seconds

DNA Sequence Alignment download



Fully functional trial


This trial version is fully functional except the saving the contig to disk (the contig is saved, but advertisement is inserted over its bases). When the trial period ends, you can still use DNA Baser Assembler to:

  • Edit and view chromatograms
  • Cut primers
  • Assemble contigs
  • Reverse complement sequences
  • Convert between ABI, SCF, FASTA, GBK, etc formats



What's new since v3?


DNA Baser Assembler v5 brings over 350 new features and improvements:

  • 64 bit support. DNA Sequence Assembler can now assemble much much longer contigs! The amount of available RAM is now the only limitation.
  • 'Highlight IUPAC bases' function in grid
  • 'Show original bases' function in chromatogram
  • MUCH better handling for corrupted SCF/ABI files
  • Improved QV assesment for SCF files
  • Improved 'Batch assembly by subfolders'
  • Mutation detection: single/multiple organisms, multiploid/diploid/haploid
  • Advanced SNP detection - Offers you the most accurate solution on the market.
  • Automatic homopolymers error correction
  • Chromatogram preview in Project manager
  • One click chromatogram overview
  • Accurate internal base caller
  • Tasks-based interface
  • Even better sequence assembler and automatic end trimming
  • Full support for IUPAC ambiguity code

See full list of features here



Did you know


that you can integrate DNA Baser Assemler in your own pipeline by calling it from your script/ command line/ program?


Our customers


DNA Sequence Assembler was cited in thousands of scientific articles and is used by countless companies and research institutions all over the world.



Price list


DNA Baser price starts at $69.



Quick links


Hardware requirements


The hardware requirements are really modest:

  • Any computer with 1GB RAM will do it
  • 0.02 GB free disk space

Privilege required for installation

  • You don't need administrator privileges in order to install the software. Anyone can install it, anywhere.
  • DNA Sequence Assembler does not install libraries, updates, DLL, Java or registry keys into your system.


DNA sequence alignment box


Microsoft Windows Installing DNA Sequence Assembler on Windows

DNA Sequence Assembler is compatible with ALL modern Windows editions (Windows XP, Windows Vista, Windows 7, Windows 8, Windows 10).


Mac OS XLinuxInstalling the sequence assembler on Mac/Linux


Even if DNA Sequence Assembler is a native Windows application it can run indirectly on Mac and Linux. However, officially, we can only support Windows users.



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Name   Description
DNA Sequence Assembler
DNA Sequence alignment
DNA Baser is a tool for DNA Sequence Assembler, DNA sequence analysis, contig editing, and mutation detection. It also offers a powerful chromatogram viewer/editor.

DNA Baser

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A Batch DNA Sample Converter
DNA Sequence Assembler is now available soon also as a command line tool so you can call it from your own code/scripts. Price $99.



multi-FASTA to FASTA

DNA Chromatogram Explorer is a Windows Explorer clone dedicated to DNA sequence analysis and manipulation. You can view the chromatograms while browsing through folders using its integrated file explorer. With a single click you can trim the low quality bases at the end of your samples.

GBK to FASTA converter
GBK to FASTA converter freeware
GenBank to FASTA is a freeware program will convert GenBank (gbk) file format to FASTA format.
ABI to FASTA converter
ABI to FASTA Converter
ABI to FASTA Converter is a free tool will convert all (selected) ABI files to FASTA files. All you need to do is to locate your ABI chromatogram files and press the CONVERT button.
Grid cell counter
Grid cell counter Gird cell counter will help you to count faster the cells shown on computer's screen by displaying a grid over your image. Freeware.
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.
DNA Counter
DNA Counter DNA Counter shows the proportions between nucleotides in a DNA sequence (GC to AT ratio).
Everything to FASTA converter
multi-FASTA to FASTA

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.

100% virus free All programs have been scanned against viruses.




Previous releases


To download previous versions or alternate releases, click here.




contig assembly software
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