Some alternatives to using Alscript

A list of sequence analysis programs that are maintained locally.

For those looking for alternative software for making colour alignments, try the web-based applications, Boxshade, Cinema, or webESPript.

  • examples of Cinema "mailback postscript" files - DNA - Protein

PC (i.e. Windows) users can also check out some freeware applications such as GeneDoc, or BioEdit. MacIntosh users can take a look at MacBoxShade or SeqVu, both available from Indiana Univeristy's archive.

Another alternative is to use the document preparation system known as TeX/LaTeX, which is available on UVa IBM/AIX machines (see ITC's web page for documentation on LaTeX).

LaTeX is also included with virtually all Linux distributions, such as RedHat, ManDrake, and SuSe.

There is a TeX macro-package available, called TeXShade, intended for preparing colour/shading/annotated molecular alignments.

Windows users can download a binary version of LaTeX, known as MiKTeX, and use TeXShade on their desktop PCs.

Apple OS X users can install freeware copies of TeX/LaTeX, most easily through one of the open source package manager suites, FINK or MacPorts (formerly DarwinPorts).

I do not know of any freeware ports of LaTeX for the Mac OS 9, but there are shareware ports available, such as OzTeX and CMacTeX, as well as commercial software such as Blue Sky Research's TexTures. OS X users may install LaTex editors (Lyx, TexMacs) from source, or use the package manager FINK.

Please email comments or suggestions about the ACHS MolBiol pages to mblack@virginia.edu.

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