Hi, Using my windows machine I was able to use Clustalo command line tool to conduct MSA on 1,000 different protein sequences (around 30 - 40 A.A long). At this point I wish to use the aligned output to produce a phylogeneitc tree. I would love to hear recomendations on which tool would be the best fit for this job? I plan on using more sequences in the future so a tool which can handle bigger scales of work has an advantage.
i recommendusing linux and cmd :)