NAME

biopop - Wrapper script for Bio::Perl's population genetics modules

SYNOPSIS

biopop options [alignment_file]

biopop [-h | --help | --v | --version --man]

DESCRIPTION

Wrapper script for Bio::Perl's population genetics modules: use Bio::PopGen::Utilities; Bio::PopGen::Statistics, and Bio::PopGen::Population;

OPTIONS

--distance, -d

Calculates a distance matrix for all pairwise distances of all sequences in the input alignment and prints it out.

Use --dist-method to specify the method desired. The default in Bio::Align::DNAStatistics is "JukesCantor".

--dist-method, -D

Used with --distance to specify which distance method to use when getting the distance matrix.

Program quits if the distance method is invalid

--heterozygosity, -H

Foreach segregating site(s), the observed heterozygosity is returned.

--input, -i

Input file format. By default, this is 'clustalw'.

--mismatch, -m

Pairwise calculation of mismatches for all sequences in the alignment.

--numseq, -n

Input file format. By default, this is 'clustalw'.

--pi, -p

Nucleotide Diversity is a measure of genetic variation or differences. It is similar to expected heterozygosity. This method takes in an alignment and outputs an integer.

--stats, -s <comma separated list of values>

Specify the statistics you would like to gather from input data. e.g., "theta,pi" will calculate the theta and pi values.

Can also be specified by giving the option multiple times. e.g., biopop --stats=pi --stats=theta

--snp_coding

Identify & print, for each 2-state SNP, codon position, aligned nucleotide position, syn/nonsyn, frequencies of each allleic state, for a coding alignment.

--varsites, -v

This method outputs the number of segregating or SNP sites within your alignment.

Common Options

--help, -h

Print a brief help message and exit.

--man

Print the manual page and exit.

--version, -V

Print current release version of this command and exit.

CONTRIBUTORS

• Yözen Hernández yzhernand at gmail dot com

• Weigang Qiu (Maintainer)

• Rocky Bernstein