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.
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),
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.
HHMI/Department of Genetics
Washington University School of Medicine
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St Louis, MO 63108 USA
FAX : 1-314-362-2157