CodonCode Corporation offers Windows versions of Phrap, Phred, and Cross_match, Phil Green's programs for fast sequence assembly, better base calling, and fast sequence comparisons.
Phred, Cross_match, and Phrap are supplied as individual executables (".exe" files) that run native under Windows95, Windows98, and WindowsNT. Except for running native under Windows, the programs are identical to their Unix counterparts - which means they are run from the command line (MS-DOS windows), and parameters are specified as command line options.
Most Windows users expect to run programs through a graphical user interface rather than from the command line; furthermore, they need a contig viewer and editor to look at assembly results. For those users, CodonCode Corporation has developed the sequence assembly and alignment software CodonCode Aligner.
CodonCode Aligner offers support for running Phred and Phrap, as well as many other commonly used functions like end clipping, vector trimming, mutation detection, contig alignments, and more. Free demo and trial versions are available for downloading, and include installers of time-limited trial versions of Phred and Phrap.
Phrap and Phred have gained the position as the prefered tools for sequence assembly and base calling at many large scale sequencing projects because of the advanced algorithms the programs offer. Now, Phred and Phrap are available to users who prefer to use familiar Windows computers. The programs run very fast on current computers - on 300 MHz PCs, Phred typically processes sequence traces in less than a second per trace, and Phrap can assembly cosmid- to BAC-sized sequencing projects in minutes.
Fast Phrap assemblies can become critical as projects grow. Our early customers found that the Phred - Phrap package is much more adequate than currently available PC software for medium-sized sequencing projects. For example, an EST project with more than 1000 reads (and more reads coming in every day) was stretching the limits of other PC software for sequence assembly - but assembled easily using CodonCode's Phrap for Windows.
In other applications, the highly accurate, base-specific Phred quality scores are very useful. Phred quality scores are commonly used to compare different sequencing methods; they are also very useful to differentiate between real mutations and random errors in evolutionary and mutation detection studies.