import numpy
import scipy
import scipy.stats

  ~/pyrad_v.2.0/pyRAD -n

  ~/pyrad_v.2.0/pyRAD -h

   ~/pyrad_v.2.0/pyRAD -p params.txt

  ~/pyrad_v.2.0/pyRAD -p params.txt -s 1

  ~/pyrad_v.2.0/pyRAD -p params.txt -s 234567 

  ~/pyrad_v.2.0/pyRAD -p params.txt -s 7

from IPython.core.display import SVG 
SVG('https://dl.dropboxusercontent.com/u/2538935/PYRAD_TUTORIALS/figures/datatypes.svg')

from IPython.core.display import Image 
Image('https://dl.dropboxusercontent.com/u/2538935/PYRAD_TUTORIALS/figures/dotLoci_single.png')

Image('https://dl.dropboxusercontent.com/u/2538935/PYRAD_TUTORIALS/figures/dotLoci_pairs.png')

Image('https://dl.dropboxusercontent.com/u/2538935/PYRAD_TUTORIALS/figures/dotPhy.png')

Image('https://dl.dropboxusercontent.com/u/2538935/PYRAD_TUTORIALS/figures/dotNex.png')

Image('https://dl.dropboxusercontent.com/u/2538935/PYRAD_TUTORIALS/figures/dotAllele.png')

Image('https://dl.dropboxusercontent.com/u/2538935/PYRAD_TUTORIALS/figures/dotSNPs.png')

Image('https://dl.dropboxusercontent.com/u/2538935/PYRAD_TUTORIALS/figures/dotUSNPs.png')

>A     CCRACACAGAGGGCCAATAGACACGTAGCTCGAGATCTCACCGCCCCCGCGATCT
>B     CCRACACAGAGGGCCAATAGACACGTAGCTCGAGATCTCACCGCCCCCGCGATCT
>C     CCRACACAGAGGGCCAATAGACACGTAGCTCGAGATCTCACCGCCCCCGCGATCT
>D     CCRACACAGAGGGCCAATAGACACGTAGCTCGAGATCTCACCGCMCCCGCGATCT
>E     CCRACACAGAGGGCCAATAGACACGTAGCTCGAGATCTCAGCACCCCCGCGATCT
>F     CCAACACAGAGGGCCAATAGACACGTAGCTCGAGATCTCAGCAACCCCGCGATCT
//%P     *                                       *--          |
>A     CGTACAATAGGATGCACCGTTCGTAAAGTTCTTGACGGTGGACCGAGAACTAGGT
>B     CGTACAATAGGATGCACCGTTCGTAAAGTTCTTGACGGTGGACCGAGAACTAGGT
>C     CGTACAATAGGATGCACCGTTCGTAAAGTTCTTGACGGTGGACCGAGAACTAGGT
>D     CGTACAATAGGATGCACCGTTCGTCAAGTTGTTGACGGTGGACCGAGAACTAGGT
>D     CGTACAATAGGATGCACCGTTCGTCAAGTTGTTGACGGTGGACCGAGAACTAGGT
//%D                           -     -                        |
>A     CGTACAATAGGATGCACCGTTCGTAAAGTTCTTGACGGTGGACCGAGAACTAGGT
>B     CGTACAATAGGATGCACCGTTCGTAAAGTTCTTGACGGTGGGACGGACGGACGGA
>C     CGTACAATAGGATGCACCGTTCGTAAAGTTCTTGACGGTGGGACGGACGGACGGA
>D     CGTACAATAGGATGCACCGTTCGTCAAGTTGTTGACGGTGGACCGAGAACTAGGT
//%S                           -     -          **  *******  *|
...

SVG("https://dl.dropboxusercontent.com/u/2538935/PYRAD_TUTORIALS/figures/twostep2.svg")