- alistat - show statistics for a multiple alignment file
alistat [options] alignfile
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
- 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.
- 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
- Print brief help; includes version number and summary of all options,
including expert options.
- be quiet - suppress the verbose header (program name, release number and
date, the parameters and options in effect).
- (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.
- --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.
afetch(1), compalign(1), compstruct(1), revcomp(1),
seqsplit(1), seqstat(1), sfetch(1), shuffle(1),
sindex(1), sreformat(1), stranslate(1), weight(1).
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
HHMI/Department of Genetics
Washington University School of Medicine
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FAX : 1-314-362-2157