SIMPLE SOLUTIONS

# ALISTAT(1) - man page online | user commands

Show statistics for a multiple alignment file.

Chapter
January 2003
```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 for‐
mat (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 pre‐
fixed 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 cho‐
sen, 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 for‐
mat.  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).

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 COPY‐
ING 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: @genetics.wustl.edu

Biosquid 1.9g                              January 2003                                alistat(1)```
 This manual Reference Other manuals alistat(1) referred by afetch(1) | compalign(1) | compstruct(1) | revcomp(1) | seqsplit(1) | seqstat(1) | sfetch(1) | shuffle(1) | sindex(1) | sreformat(1) | stranslate(1) | weight(1) refer to afetch(1) | compalign(1) | compstruct(1) | revcomp(1) | seqsplit(1) | seqstat(1) | sfetch(1) | shuffle(1) | sindex(1) | sreformat(1) | stranslate(1) | weight(1)