Phylogeny
Depends if you want to bootstrap the tree. If you don´t, it should be pretty quick, as NJ is a very fast algorithm.
Without bootstrapping only for complete alignment ,I did run one a day ago on ClustalX using FASTA format total nucleotide sequence are about 26MB and its still running.
Maybe if you can share your file through dropbox, or otherwise, I can try it out for you.
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