texshade – Pack­age for set­ting nu­cleotide and pep­tide align­ments

TeXshade is align­ment shad­ing soft­ware com­pletely writ­ten in TeX/LaTeX; it can pro­cess mul­ti­ple se­quence align­ments in the .MSF and the .ALN file for­mats. In ad­di­tion to com­mon shad­ing al­go­rithms, it pro­vides spe­cial shad­ing modes show­ing func­tional as­pects, e.g. charge or hy­dropa­thy, and a wide range of com­mands for han­dling shad­ing colours, text styles, la­bels, leg­ends; it even al­lows the user to de­fine com­pletely new shad­ing modes. TeXshade com­bines high­est flex­i­bil­ity with TeX out­put qual­ity — all in a bun­dle that does not de­mand ex­ces­sive de­vel­op­ment time of the user.