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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 outlying sequence).


-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.


--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.

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