alistat(1)							  Biosquid Manual							alistat(1)

NAME

       alistat - show statistics for a multiple alignment file

SYNOPSIS

       alistat [options] alignfile

DESCRIPTION

       alistat	reads  a  multiple sequence alignment from the file alignfile in any supported format (including SELEX, GCG MSF, and CLUSTAL), and
       shows a number of simple statistics about it.  These statistics include the name of the format, the number of sequences, the  total  number
       of residues, the average and range of the sequence lengths, the alignment length (e.g. including gap characters).

       Also  shown are some percent identities. A percent pairwise alignment identity is defined as (idents / MIN(len1, len2)) where idents is the
       number of exact identities and len1, len2 are the unaligned lengths of the two sequences. The "average  percent	identity",  "most  related
       pair",  and  "most unrelated pair" of the alignment are the average, maximum, and minimum of all (N)(N-1)/2 pairs, respectively.  The "most
       distant seq" is calculated by finding the maximum pairwise identity (best relative) for all N sequences, then finding the minimum of  these
       N numbers (hence, the most outlying sequence).

OPTIONS

       -a     Show  additional	verbose  information: a table with one line per sequence showing name, length, and its highest and lowest pairwise
	      identity. These lines are prefixed with a * character to enable easily grep'ing them out and sorting them. For example,  alistat	-a
	      foo.slx | grep * | sort -n +3 gives a ranked list of the most distant sequences in the alignment.  Incompatible with the -f option.

       -f     Fast;  use a sampling method to estimate the average %id.  When this option is chosen, alistat doesn't show the other three pairwise
	      identity numbers.  This option is useful for very large alignments, for which the full (N)(N-1) calculation of all  pairs  would	be
	      prohibitive (e.g. Pfam's GP120 alignment, with over 10,000 sequences). Incompatible with the -a option.

       -h     Print brief help; includes version number and summary of all options, including expert options.

       -q     be quiet - suppress the verbose header (program name, release number and date, the parameters and options in effect).

       -B     (Babelfish).  Autodetect	and  read a sequence file format other than the default (FASTA). Almost any common sequence file format is
	      recognized (including Genbank, EMBL, SWISS-PROT, PIR, and GCG unaligned sequence formats, and Stockholm, GCG MSF, and Clustal align-
	      ment formats). See the printed documentation for a complete list of supported formats.

EXPERT OPTIONS

       --informat <s>
	      Specify  that the sequence file is in format <s>, rather than the default FASTA format.  Common examples include Genbank, EMBL, GCG,
	      PIR, Stockholm, Clustal, MSF, or PHYLIP; see the printed documentation for a complete list of accepted format  names.   This  option
	      overrides the default format (FASTA) and the -B Babelfish autodetection option.

SEE ALSO

       afetch(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), stranslate(1),
       weight(1).

AUTHOR

       Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under  the  GNU
       General Public License (GPL) See COPYING in the source code distribution for more details, or contact me.

       Sean Eddy
       HHMI/Department of Genetics
       Washington University School of Medicine
       4444 Forest Park Blvd., Box 8510
       St Louis, MO 63108 USA
       Phone: 1-314-362-7666
       FAX  : 1-314-362-2157
       Email: eddy@genetics.wustl.edu

Biosquid 1.9g							   January 2003 							alistat(1)