# Align.pl - Manual

## Command Line Options

    Mode switch (case-insensitive)
    -blast            add BLAST match HSPs to alignment project
    -h(elp)           output command line syntax description and exit
    -session          alignment project session (default mode).

    ModeSwitch (case-insensitive)
    -BlastLimit=N     limit BLAST search to first N BLAST hits
    -debug(=N)        print debug protocol to STDOUT/STDERR
                      N           debug depth value
    -log(=S)          redirect STDOUT and STDERR to LOG file.
                      S           log file path, default path worked out
                                  automatically from built-in directives.
    -noDB             don't refer to original sequence data from the database.
                      this switch doesn't work with the ModeSwitch -Session.
    -OutImgTransp     turn image's background transparent
    -OutImgWidth=N    define the output image's pixel width
    -script           for mode '-session' this option forces the program to behave
                      like an interpreter rather than a command line console. No
                      prompt is printed out and dialogue functions are suppressed.
    -timer            print time-performance protocol to STDOUT.
    -v(erbose)        print extended progress report to STDOUT.

## Session Commands

    add [...]
    Add sequence (stretch) into alignment.

    append <end> <ProjectDescr>
    Add another alignment at the alignment end.

    close
    [planned:] Close project (like command 'exit') but keep AlnK shell running.

    dismiss
    Exit user session. Leave the program discarding any changes that may have
    been made to the open project (cmp. command 'exit').

    edit <opt:uncond> <opt:1block>
    Edit alignment (via nedit at the moment). Option 'uncomp' switches off the
    condense feature. Given option '1block' the alignment is shown in one big
    Pearson block.

    exit
    Exit user session. You're asked if you want to save changes if you've
    made some (cmp. command 'dismiss').

    fasta <filename>
    Export des Alignments als fastA-File in die Datei <filename>.

    hide
    Hide extensions of sequence stretches in the alignment (cmp. command
    'show').

    logo
    prepare LOGO picture (PostScript format) showing the information content
    in the aligned sequences for each position.

    matrix
    Calculate a log(frequency) matrix for the alignment or range of the
    alignment. Print it to STDOUT.

    name <ProjName>
    Rename alignment project.

    print <opt:RangeOff> <opt:RangeEnd> <opt:'consensus'> <opt:'id'>
    Output of the alignment in clustal W format. Optionally, you can specify
    a range of the alignment that's desired for output (numerical arguments
    <RangeOff> and <RangeEnd>). The optional argument 'consensus'
    forces the program to print only the consensus sequence in fastA format.
    The optional argument 'id' tells the program to print the sequence
    identifiers of all the entries of the alignment.

    report <ReportType>
    Do a report about the alignment project. Following report types are
    supported:
    align    prepare table containing positional data for each alignment entry.
    cover    plot coverage value over the alignment
    diverg   prepare table containing data on divergence from consensus for each
             alignment entry
             ConsDev        table of polymorphic alignment positions
             ConservEntrop  plot of local symbol entropy
             FrameShift     plot of deviations producing frameshifts
             LocalMatscore  plot of local distance according to pairwise distance
                            matrix
             PairwDist      table of pairwise distances
             SmbFreq        symbol frequency table
             unique         plot of local sequence uniqueness
    ?ids     list of sequence identifiers
    param    list alignment project parameters
    statist  list statistics about the sequence distribution in the alignment
             as well as in the sequence source pool

    resolveunk
    Resolve unknown symbols in sequences.

    revcompl
    Change project to reverse-complement.

    save <filename> [-force 1]
    Speichern des Projekts unter dem Projekt-Pfad (filename = '') oder dem angege-
    benen Pfad filename. Mit Option -force wird die User-Interaktion beim Über-
    schreiben von existierenden Files unterdrückt. User-Interaktion findet
    grundsätzlich nicht statt, wenn Programmoptionen -log oder -script gesetzt
    sind.

    show <opt:[+-]?range> <opt:end>
    Show extension of sequence stretches in the alignment.
    By parameter 'range' you may direct stretch ends and length of the
    extensions to appear in the alignment. An optional sign preceding the
    range value specifies which stretch end to be extended (-: left, +: right).
    Indepently, you may specifiy the end to be extended as a separate argument
    ('left' or 'right').
    The extensions are represented in lower-case letters in contrast
    to the real alignment representation which is in upper case.

    sort <opt:directive>
    Sort alignment entries.

    split <Len5end>
    Split alignment project into halfs.

    validate
    Revert extensions of sequence stretches to status 'valid'.

## Data structure for Alignment Projects

    see inline documentation in under &SeqAlign::AlnProj::AlnprojClustalOpen.