[Biojava-l] How to get guide tree,root MSA and lineage file

[Muhammad Tariq Pervez]

hi all,
I am working on a research project. To build simulated/true MSA through iSG2.1 is its part. But i don't how to get/build guide tree, root MSA and lineage files. These files are basic requirements of iSG for building true alignment. Guide trees are built by almost all MSA methods but i am confused what guide tree should be used for iSG and what is root MSA etc.
Your help will be very beneficial for the research work.

Best Regards.


Muhammad Tariq Pervez

Ph.D (Bioinformatics Scholar)