ESPript: a program which renders sequence similarities and secondary structure information from aligned sequences
Recently, I found a nice program which can take the results of multiple seuqence alignments and secondary structure information as input and then generate nice figures for analysis and publication. Here is an example shown in their web site: What is ESPript? ESPript , 'Easy Sequencing in PostScript' , is a program which renders sequence similarities and secondary structure information from aligned sequences for analysis and publication purpose. How to generate multiple alignments? To generate multiple sequence alignments, there are various tools you can use. I usually use MUSCLE, MAFFT and ClustalW. How to get secondary structure information? To get secondary structure information, you can search the information on the the Protein Data Bank ( PDB ).