Hi there! I'm looking for a solution to the following problem: When aiming to generate multiple png figures of different MSAs, one prefers to rely on the command line usage of Jalview. Using the feature file (-features argument) should help to define user-specific annotations on an MSA. My goal is to highlight 2 columns with a random color (e.g. red) in each alignment. Although the feature file enables me to color amino acids in each sequence at the defined positions, I'm running into trouble when there are gaps at these positions of interest. The coloring is then shifted to the neighboring amino acids... Did someone have the same issue??
Sunny greetings, Martina Martina Weigl PhD candidate, Bioinformatics Wissenschaftszentrum Weihenstephan, Technische Universität München Maximus-von-Imhof-Forum 3, 85354 Freising, Germany Email: martina.we...@mytum.de
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