I have used a boxshade server, but here I am finding difficulties as it puts sequence numbers here and there after the job. So does anybody have an idea to do the same without any erroneous job of the programme. Any programme which does this and can be used for the purpose of publishing articles.
Please suggest.
Just adding another option: http://espript.ibcp.fr/ESPript/ESPript
Try Jalview, which is a free program for MSA editing, visualisation and analysis (www.jalview.org).
TEXshade: shading and labeling of multiple sequence alignments using LATEX2 epsilon.
reference code:
\begin{texshade}{AQPpro.MSF}
\threshold[80]{50}
\setends{1}{80..112}
\showconsensus[ColdHot]{bottom}
\defconsensus{.}{lower}{upper}
\showlegend
\end{texshade}
http://bioinformatics.oxfordjournals.org/content/16/2/135.long
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