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.
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: [email protected]