I am looking for a software, quite user friendly, for character data and genomic sequence. It should be didactic and help for learning phylogenetic analysis.
I look at Mesquite but it seems rather complex to use and not very often cited.
I look also to Paup, often cited, but appear quite outdated.
There is more in looking to the web.
You should check MEGA - Molecular Evolutionary Genetics Analysis. It implements a number of phylogenetic routines and provides a user-friendly GUI.
http://www.megasoftware.net
I think Jalview is very useful for colorful presentation of your sequences
https://www.researchgate.net/publication/268686920_Building_a_Multiple_Sequence_Alignment_%285%29_%28Editing__Coloring_using_Jalview%29
Conference Paper Building a Multiple Sequence Alignment (5) (Editing & Colori...
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