alistat [options] alignfile
- alistat - show statistics for a multiple alignment
reads a multiple sequence alignment from the file
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))
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).
- 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 -a option.
- 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.
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
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