alnpi - calculate molecular population genetic statistics from DNA alignments
alnpi [OPTIONS] [MULTIFASTA-FILE...]
alnpi takes multifasta format alignment data as input, and outputs molecular population genetic statistics. Options modulate the type of statistics calculated, the mode of calculation, and the style of output. By default, per-site statistics are calculated over the entire output, specifically after gap-containing sites are removed. Optionally, statistics may be calculated pair-wise across sequences, or in sliding windows of specified length. The statistics calculated by default include:
Invoked in absolute mode with alnpi --absolute, alnpi outputs these statistics instead:
Sliding window analysis supports output for only for nucleotide diversity, Watterson estimator per-site, and Tajima's D.
Options specific to alnpi: -s, --suppress suppress table header output -x, --latex print table with Latex formating -p, --pairwise calculate stats pairwise across sequences -w, --window=<string> calculate stats in sliding windows --absolute output statistics not normalized per-site --label=<string> label input/output descriptively with <string>
Options general to FAST: -h, --help print a brief help message --man print full documentation --version print version -l, --log create/append to logfile -L, --logname=<string> use logfile name <string> -C, --comment=<string> save comment <string> to log --format=<format> use alternative format for input --moltype=<[dna|rna|protein] specify input sequence type
alnpi is part of FAST, the FAST Analysis of Sequences Toolbox, based on Bioperl. Most core FAST utilities expect input and return output in multifasta format. Input can occur in one or more files or on STDIN. Output occurs to STDOUT. The FAST utility fasconvert can reformat other formats to and from multifasta.
Supress header output
LaTeX-style output
Statistics are calculated pairwise over all sequences
Sliding window analysis. Option argument <string> expected to be in the form "window-size:step-size:statistic" where window-size and step-size are positive integers and "statistic" may be one of "p", "s" or "d" for nucleotide diversity, Watterson estimator or Tajima's D respectively.
Output a smaller set of statistics not normalized by number of gap-free sites.
Text label for the input data, to be placed in the output.
Print a brief help message and exit.
Print the manual page and exit.
Print version information and exit.
Creates, or appends to, a generic FAST logfile in the current working directory. The logfile records date/time of execution, full command with options and arguments, and an optional comment.
Use [string] as the name of the logfile. Default is "FAST.log.txt".
Include comment [string] in logfile. No comment is saved by default.
Use alternative format for input. See man page for "fasconvert" for allowed formats. This is for convenience; the FAST tools are designed to exchange data in Fasta format, and "fasta" is the default format for this tool.
Specify the type of sequence on input (should not be needed in most cases, but sometimes Bioperl cannot guess and complains when processing data).
Generate sliding window of Tajima's D, the data plotted in Fig. 4A of Ardell et al. (2003) Genetics 165:1761. The data files ship with FAST:
fasgrep -v "(AF194|349[06])" t/data/ArdellEtAl03_ncbi_popset_32329588.fas | alndegap | fastr --strict -a "-" | alnpi --window 100:25:d
Statistics for 5'UTRs, the last line in Table 1 of Ardell et al. (2003) Genetics 165:1761:
gbfalncut -K t/data/ArdellEtAl03_ncbi_popset_32329588.fas t/data/AF194338.1.gb 5.UTR | fasgrep -v "(AF194|349[06])" | alndegap | fastr --strict -a "-" | alnpi
man perlre
perldoc perlre
Documentation on perl regular expressions.
man FAST
perldoc FAST
Introduction and cookbook for FAST
If you use FAST, please cite Ardell (2013). FAST: FAST Analysis of Sequences Toolbox. Bioinformatics and Bioperl Stajich et al..
To install FAST, copy and paste the appropriate command in to your terminal.
cpanm
cpanm FAST
CPAN shell
perl -MCPAN -e shell install FAST
For more information on module installation, please visit the detailed CPAN module installation guide.