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 alignment 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