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The file size is really big (26.7 MB). So, I am unable to use the online web tools, as they cannot handle such large input data.

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  • $\begingroup$ Look into IQ-TREE. If you can work with R, I'd recommend phangorn to do the maximum likelihood analysis, and use write.tree() from ape to write the Newick tree(s). $\endgroup$
    – Dunois
    May 16, 2019 at 8:44

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RAxML (Stamatakis, 2014) would be a good place to start.

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