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Tutorial

- Download multidom.fasta and blastmultidom.out

  • .fasta : sequences in FASTA format (less than 256 character per line and no "U" character [to be replaced by "X"])
  • .out : BLAST results in tabulated format
  • .fnodes : list of pairs in format "family_id sequence_id"

- Build pre-families with silix

silix multidom.fasta blastmultidom.out --net > multidom_SLX.fnodes
  • 8 pre-families displayed in multidom_SLX.fnodes
PNG - 4.6 ko
  • blastmultidom.net is generated and corresponds to the similarity network represented below
PNG - 10.6 ko

NB : if you use the MPI version of SiLiX (with mpirun), you get multiple .net files that you need to concatenate into in single .net file.

- Build high-quality families with hifix

hifix multidom.fasta blastmultidom.net multidom_SLX.fnodes > multidom_HFX.fnodes
  • 9 families displayed in multidom_HFX.fnodes
PNG - 4.2 ko
  • if n are processors avalaible, use option -t n