biopop - Wrapper script for BioPerl's population genetics modules

SYNOPSIS

biopop [options] <alignment_file>

DESCRIPTION

biopop DESCRIPTION GOES HERE

OPTIONS

--help, -h

Print a brief help message and exits.

--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.

--version, -V

Print current release version of bp-utils.

Usage: bioseq -V

REQUIRES

Perl 5.010, BioPerl

SEE ALSO

  perl(1)

AUTHORS

 Weigang Qiu at genectr.hunter.cuny.edu
 Yözen Hernández yzhernand at gmail dot com

cpanm Bio::BPWrapper

perl -MCPAN -e shell
install Bio::BPWrapper