Say for example a combination of MATK and RBCL gene in plants ?
I think you can use MrBayes software (Bayesian analysis).
Hi. Please use MEGA6 tool. By using this tool you can produce different form of phylogenetics trees.
Mega6 tool link:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840312/
nowadays, BI and ML analyses are used. Sometimes, MP is also included
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