Hello, I have several questions regarding multiple sequence alignment (MSA):

1. How can I produce publication-quality MSA figure for 150 samples? At the moment, I am using JalView for viewing the alignments. I do not plan to show every detail of the alignments. I can just select a part from the whole figure and zoom it to show the main result. I have a section of an MSA file for a specific gene sequence like this below

1. Is it possible to detect the presence of any structural variation from an MSA file like the above? Because I see that people only detect single nucleotide polymorphisms from such alignments.

2. I am planning to make a figure by keeping the alignment view and the phenotypic result side by side. I have an ordered histogram for the phenotype that the gene is responsible for and I want to sort the alignments according to their phenotypic value. Is there any tool to integrate such datasets and produce a joint figure? Because I want to keep the samples in order according to their phenotypic value.

Please let me know if you have any suggestions on those questions.

Thank you.