The T E Xshade package ∗ Typesetting nucleotide and peptide alignments

Setting alignments of nucleotides and peptides for publication or presentation purposes is usually a time consuming two-step process. First, a scientific software is used for the calculation of the alignment. This is done in a few minutes. Then, in order to highlight special sequence relationships and to label positions and regions of interest a second software with high quality output capability is needed. Manipulating sequence alignments with standard word processing or graphics programs takes its time—often several hours—and simple layout changes such as re-breaking lines, say from 50 to 40 residues per line, elongate the working time considerably. TEXshade is an alignment shading software written in TEX/L ATEX which can process multiple sequence alignments in the MSF, ALN and FASTA file format. It provides in addition to common shading algorithms special shading modes featuring functional aspects, e.g. charge or hydropathy, and a plenitude of commands for handling shading colors, text styles, labels, legends and even allows the user to define completely new shading modes. TEXshade combines highest flexibility and the habitual TEX output quality—with reasonable time expenditure.