Input

  • Please upload/select a file with aligned sequence data [info]:
    input file 1:  or use example file groel.aln

  • If available, upload a PDB structure file matching the first input sequence [info]:
        PDB file: 
        or
        insert PDB ID: (e.g. 2EU1 for GroEL example file)
        specify chain: (by default the first chain is used)
        or
         auto-retrieve PDB structure file with minimum % identity [info]

click for inter-molecular input options

  • For inter-molecule analysis upload a second data file [info]:
    input file 2: 

  • If available, upload a PDB structure file matching the second input sequence [info]:
        PDB file 2: 
        or
        insert PDB ID 2:
        specify chain 2: (by default the first chain is used)
        or
         auto-retrieve PDB structure file 2 with minimum % identity [info]

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Parameters

click to change defaults
  • tree file [info]


  • tree file 2 [info]


  • bootstrap value (0 <= 1) [info]


  • gap threshold (0 <= 1) [info]


  • alpha threshold (0 <=1) [info]


  • number of alignments to simulate (we recommend 100 unless your data is somewhat irregular) [info]


  • await convergence [info]
    on
    off

  • time correction [info]
    on
    off

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Submission

Click the button to start the analysis:   

Optionally, provide an e-mail address: [info]



kahokamp@tcd.ie