sequence assembly
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scf trace assembly
DNA contig assembly

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

sequence assembling software

 

Sanger/short contig bioinformatics tools

 

sequence assembly DNA Baser Sequence Assembler  
 

DNA Baser Sequence Assembler is unique and revolutionary bioinformatics software for

Instant download

The ultimate DNA sequence analysis & assembly software

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

Chromatogram Explorer

  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.

 

Freeware

Sequence dereplicator

sequence assembler

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.

 

 

 

Freeware

Grid cell counter

 

 

 

 

NextGen bioinformatics tools


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

 

NextGen SFF/FastQ Workbench new
 

An efficient and easy to use FastQ/SFF viewer, editor and converter. NextGen Workbench is the first and only complete FastQ/SFF editor with graphic interface on the entire bioinformatics market! With this tool we wanted to help the biologists to concentrate on their work instead of wasting time poking commands in an obscure text console. The program can open huge FastQ/SFF files even when running o a modest computer.

Freeware

 

NCBI Blast DB Downloader new
 

Easy NCBI Blast DB Downloader is a a freeware biology software tool that automates the NCBI BLAST DB download process.

 

Freeware

Download-DNA sequence analysis and assembly software

 

NCBI BLAST Robot new
 

is a a freeware molecular biology software tool that automates the NCBI BLAST alignment of coding DNA or protein sequences and processes the results for visualization. The program seamlessly integrates with DNA Baser Sequence Assembler. It collects the contigs generated during manual or automatic (batch) sequence assembly, sends queries to NCBI Blast server and automatically download the results (the GBK files) to disk then it helps the user to analyze its data.

 

Freeware

NCBI Blast automation tool

 

 

 

Other tools

 

DNA Baser console  
 

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.

 

 

Download page

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


pause > nul

sequence assembler

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).

 

 

Download page

Article

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

 

 

Download page

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. Protein FASTA files are also supported.

 

 

Freeware

multi-FASTA to FASTA converter

 

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.

 

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

GBK to FASTA converter

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

DNA Nucleotide Counter

 


 

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'.

 

 

Portability

 

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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