1) *.cds.fasta is DNA alignment in FASTA format; *.ml.tre is ML tree based on overlapping regions only.
2)Sequences were named as species plus unigene id, e.g. lgn_219008 represents tomato unigene 219008 (SGN build).  "stgn_" stands for potato, "cangn_" for pepper and "cgn_" for coffee.
