NAME

       squizz - Sequence format checker" 4

SYNOPSIS

       squizz [-AShlnsv] [-c format] [-f format] file

OPTIONS

       Following command line options are allowed:

       -A  Restrict detection/verification to alignment formats (conflict with -S option).

       -S  Restrict detection/verification to sequence formats (conflict with -A option).

       -c format
           Convert detected sequence/alignment into format. This option implies strict alignment checking.

       -f format
           Assume  input  format  is  format. Do not try to detect the format, just verify that the given one is
           correct.

       -h  Display help message and exit.

       -l  List all supported formats.

       -n  Count and report detected entries. This option is only available when the detection is restricted  to
           a single type (with -A or -S options) and strict checks (without -s option) are enabled.

       -s  Disable strict format checks (enabled by default).

       -v  Display version information and exit.

DESCRIPTION

       squizz is a sequence format file checker, but it has some conversion capabilities too.

       squizz can detect the most common sequence and alignment formats :

       * CODATA, EMBL, FASTA, GCG, GDE, GENBANK, IG, NBRF (pir), RAW, and SWISSPROT.

       * CLUSTAL, FASTA, MSF, NEXUS, PHYLIP (interleaved and sequential) and STOCKHOLM.

       squizz  can  do  some  conversions  too,  if  the  format the input format is supported. Only 3 types are
       available : sequence to sequence, alignment to alignment,  and  alignment  to  sequence  (the  last  one,
       sequence  to  alignment,  require  multiple  alignments  algorithms and cannot be handled with formatting
       tools).

       Strict format checks validate the previously detected objects, by making some sanity checks:

       - sequence strings must exists.
       - alignment is made of more than one sequence.
       - alignment sequence strings must have the same length.
       - alignment sequence names must exists, and be unique.

SEE ALSO

       seqfmt(5), alifmt(5)

AUTHOR

       Nicolas Joly (njoly@pasteur.fr), Institut Pasteur.

Unix                                               2015-09-21                                          SQUIZZ(1)