[modeller_usage] how to create .ali file

Dear all,

Psiblast search could find a template for my protein sequence with low identity (19%). So i preferred mgenTHREADER. I got the alignment results form genthreader. Now i don't know how to create the .ali file i have a aligned text file and .aln file. Now what is command for creating the .ali file and what are the files i need to make changes in the files (scripts) with my own target sequence.

But the psiblast hit and the mgentreader results are not the same. Can I trust the mgenthreader results.?

thanks in advance

sankari

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