jasonsahl

#The input is two colums: x and corresponding y values
require(MASS) ## for mvrnorm()
set.seed(1)
mine <- read.table("xy.txt")
mine <- data.frame(mine)
names(mine) <- c("X","Y")
plot(mine)
res <- resid(mod <- lm(Y ~ X, data = mine))
res.qt <- quantile(res, probs = c(0.001,0.999))
want <- which(res >= res.qt[1] & res <= res.qt[2])

jasonsahl

#!/usr/bin/env python

"""retrieve only parsimony infomative
sites from a nucleotide multiple sequence alignment"""

from optparse import OptionParser
import sys
try:
    from Bio import SeqIO
except:

jasonsahl

#!/usr/bin/env python

from __future__ import division
"""calculates the SNP and homoplash density
using a NASP formatted SNP matrix"""


import optparse
import sys
import collections

jasonsahl

#!/usr/bin/env python

"""filter a NASP formatted SNP
matrix, to only include a list of genomes.
The collections module requires Python 2.7+.
This script has not been tested with Python 3"""

from optparse import OptionParser
from collections import deque
import sys