Ridom TraceEdit is a cross-platform graphical DNA trace viewer and editor. TraceEdit displays the chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format. Incorrect base calls can be edited and saved. TraceEdit is freely available and designed to operate on Windows, MacOS X and UNIX platforms.

Chromas Lite is freeware and may be distributed without restriction provided that it is unmodified and is in the form of the installer downloaded from the link above.

4Peaks is a free program for Macs that helps molecular biologists to visualize and edit their DNA sequence files.

The free Sequence Scanner Software enables you to view, edit, print and export sequence data generated using the Applied Biosystems Genetic Analyzers.

The Ensembl trace repository provides a permanent archive for single-pass DNA sequencing reads and associated traces and quality values. These data come from whole-genome shotgun projects, EST projects, and other large-scale sequencing projects.

Trace archive at NCBI

Merge two overlapping sequences

Detection of Frameshift Sequencing Errors

The mira genome fragment assembler is a specialised assembler for sequencing projects classified as 'hard' due to high number of similar repeats. For EST transcripts, miraEST is specialised on reconstructing pristine mRNA transcripts while detecting and classifying single nucleotide polymorphisms (SNP) occuring in different variations thereof.

ESSEM stands for Est's aSSEmbly using Malig; Online tool.

Phrap is a program for assembling shotgun DNA sequence data. Among other features, it allows use of the entire read and not just the trimmed high quality part, it uses a combination of user-supplied and internally computed data quality information to improve assembly accuracy in the presence of repeats, it constructs the contig sequence as a mosaic of the highest quality read segments rather than a consensus, it provides extensive assembly information to assist in trouble-shooting assembly problems, and it handles large datasets. Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap.

The AMOS consortium is committed to the development of open-source whole genome assembly software. The project acronym (AMOS) represents our primary goal -- to produce A Modular, Open-Source whole genome assembler.

Arachne is a tool for assembling genome sequences from whole genome shotgun reads, mostly in forward-reverse pairs obtained by sequencing clone ends.

Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.