Getting Started

  • ppalign

  • ppblast

    • ppalign

         ppalign  [--marg_decode] [--sampling_show_all] [--sampling_seed
              ] [--sampling ] [--expected] [--ext
              ] [--open ] [--match ] [--mismatch
              ] [-s ] [--full] [-t
              ] [--algo ] [--restrict_end ] [--restrict_start ] [--optimize ]
              [--html_align_id ] [--html_no_param]
              [--html_only_result] [--html_img_dir ] [-o
              ] [--no_line_break] [-f ] [-i
              ] [-a ] [--] [--version] [-h]

    --helpDisplays usage information and exits.
    --versionDisplays version information and exits.
    --ignore_rest
    --    		Ignores the rest of the labeled arguments following this flag.
    Input options
    -a <nucl|aa>
    --alphabet <nucl|aa>    		Select a predefined alphabet among "nucl" or "aa".
    If not provided, try to automatically detect the alphabet from the input sequences.
    -i <filename>
    --input <filename>    		Fasta file with alignment or pair of sequences.
    If filename is not provided read data from standard input.
    If the --optimize argument is NOT the given input is interpretated as an alignment. The length of both sequences must be equal in this case and they may contain the gap symbol '-'. Supply local alignments by inserting gaps at the begin and end.
    Otherwise, if --optimize is provided, the input is interpretated as a pair of sequences.Firstly the optimal alignment is determined according to the option --optimize.
    --optimize <global|global_bound|local>Assume that the input (-i or standard input) is a pair of unaligned sequences. If --optimize is provided ppalign firstly determines the optimal alignment and passes it to the main algorithm.
    Use --optimize global to determine the Needleman-Wunsch global alignment.
    Use --optimize global_bound to determine the Needleman-Wunsch global alignment with the constraint that the alignment must start and end in a pair state.
    Use '--optimize local to determine the Smith-Waterman local alignment.
    --restrict_start <i1 j1>
    --restrict_end <i2 j2>
    		When using the option --optimize the input sequences are restricted to the range (i1...i2) and (j1...j2) before the optimization.
    Output options
    -o <filename>
    --out <filename>    		Write the results (XML, text or HTML) to this file.
    If the argument is not given, write the result to standard output.
    Images for HTML pages are created in a newly created unique directory.
    --no_line_breakDo not wrap the lines in the reported alignments (1 line per alignment)
    -f <xml|text|html>
    --format <xml|text|html>    		Select one output format among 'xml', 'text' and 'html'.
    • xml: report result in plain XML for further analysis.
    • text: create a human readable ascii text.
    • html: create an HTML page with PNG images.
    --html_align_id <integer>Gives the alignment an ID. This is needed when different alignments are placed on a single HTML page.
    --html_no_paramSkip the param section of the HTML page.
    --html_only_resultShow only the result section of the HTML page.
    If --html_no_param is not provided the parameter section will be still included.
    --html_img_dir <dirname>The output directory for image objects in the HTML page.
    Algorithmic options
    --algo
    <global|global_bound|
    local_start>    		Alignment method for the computation. It is assumed that the user has provided an alignment in fasta format or a pair of sequences (via -i filename) for which the optimal alignment has been determined (via --optimize method).
    Use global to determine the posterior probabilities according to a global probabilistic alignment model. Alignments may start and end in a gap.If the optimal alignment has been determined via --optimize local only the aligned part is considered.
    Use global_bound to determine the posterior probabilities according to a global probabilistic alignment model which does not allow alignments start and end in gaps. If the optimal alignment has been determined via --optimize local only the aligned part is considered.
    Use local_start to determine start and end probabilities of local alignments.
    --fullPerform the computation on the full search space. Otherwise the computation is performed on a strip around the user supplied alignment (or the optimal alignment in the case that option --optimize is used).
    Using this option requires at least a quadratic time complexity.
    -t <floating point number>
    --temperature <floating point number>    		If this optional argument is supplied, use finite temperature alignment instead of pair HMM.
    Provide a temperature value to put more (large temperature) or less (small temperature) weight to suboptimal alignments.
    Alignment parameters
    --ext <integer>Gap extension penalty
    (default: 1 for nucl, 1 for protein)
    --open <integer>Gap open penalty
    (default: 2 for nucl, 11 for protein)
    --match <integer>Score for matches.
    Do not provide --matrix and --match at the same time
    The default for DNA alignment is 1
    --mismatch <integer>Score for mismatches.
    Do not provide --matrix and --mismatchat the same time.
    The default for DNA alignment is -2
    -s <matrix name>
    --scorematrix <matrix name>    		Select a score matrix (e.g. blosum62 or PAM250) for protein alignment.
    The default is blosum62.
    Alternative alignments
    --marg_decodeDetermine maximal averaged marginalized posterior alignment
    --sampling <integer>sample n alignments from the posterior distribution
    --sampling_seed <integer>seed for the random number generator
    --sampling_show_alloutput of full alternative alignments instead of fragments
    (XML only)
    --expectedCompute expected score

    ppblast

        ppblast  [--marg_decode] [--sampling_show_all] [--sampling_seed
              ] [--sampling ] [--expected] [-m
              ] ...  [--ext ] [--open ]
              [--match ] [--mismatch ] [-s ]
              [--full] [-t ] [--html_align_id
              ] [--html_no_param] [--html_only_result]
              [--html_img_dir ] [-o ] [--no_line_break]
              [-f ] [-i ] [--] [--version] [-h]

    --helpDisplays usage information and exits.
    --versionDisplays version information and exits.
    --ignore_rest
    --    		Ignores the rest of the labeled arguments following this flag.
    Input options
    -i <filename>
    --input <filename>    		Blast XML output.
    If filename is not provided read data from standard input.
    Output options
    -o <filename>
    --out <filename>    		Write the results (XML or HTML) to this file.
    If the argument is not given, write the result to standard output.
    Images for HTML pages are created in a newly created unique directory.
    --no_line_breakDo not wrap the lines in the reported alignments (1 line per alignment)
    -f <xml|text|html>
    --format <xml|text|html>    		Select one output format among 'xml', 'text' and 'html'.
    • xml: report result in plain XML for further analysis.
    • html: create an HTML page with PNG images.
    --html_align_id <integer>Gives the alignment an ID. This is needed when different alignments are placed on a single HTML page.
    --html_no_paramSkip the param section of the HTML page.
    --html_img_dir <dirname>The output directory for image objects in the HTML page.
    Algorithmic options
    --fullPerform the computation on the full search space. Otherwise the computation is performed on a strip around the user supplied alignment (or the optimal alignment in the case that option --optimize is used).
    Using this option requires at least a quadratic time complexity.
    -t <floating point number>
    --temperature <floating point number>    		If this optional argument is supplied, use finite temperature alignment instead of pair HMM.
    Provide a temperature value to put more (large temperature) or less (small temperature) weight to suboptimal alignments.
    Alignment parameters
    --ext <integer>Gap extension penalty
    If not provided, take the one in the BLAST output
    --open <integer>Gap open penalty
    If not provided, take the one in the BLAST output
    --match <integer>Score for matches.
    Do not provide --matrix and --match at the same time
    If not provided, take the one in the BLAST output
    --mismatch <integer>Score for mismatches.
    Do not provide --matrix and --mismatchat the same time.
    If not provided, take the one in the BLAST output
    -s <matrix name>
    --scorematrix <matrix name>    		Select a score matrix (e.g. blosum62 or PAM250) If not provided, take the one in the BLAST output
    Alternative alignments
    --marg_decodeDetermine maximal averaged marginalized posterior alignment
    --sampling <integer>sample n alignments from the posterior distribution
    --sampling_seed <integer>seed for the random number generator
    --sampling_show_alloutput of full alternative alignments instead of fragments
    (XML only)
    --expectedCompute expected score