armanbilge

import string
from collections import Counter

def leastFrequentLetters(s):
    C = Counter(c for c in s.lower() if c in string.ascii_lowercase)
    return ''.join(k for k in string.ascii_lowercase if C[k] == min(C.itervalues()))

armanbilge

#!/usr/bin/env ruby
Encoding.default_external = "UTF-8"

i = 0
puts STDIN.read.sub(/(WEBVTT\s+)(\d{2}:)/){|s| "#{$2}"}.gsub(/(\d{2}:\d{2})\.(\d{3}\s+)-->(\s+\d{2}:\d{2})\.(\d{3}\s*)/) { |s|
  "#{i+=1}\n#{s.sub(/(\d{2}:\d{2})\.(\d{3}\s+)-->(\s+)(\d{2}:\d{2})\.(\d{3}\s*)/){|t| "00:#{$1},#{$2}-->#{$3}00:#{$4},#{$5}"}}"
}

armanbilge

#!/usr/bin/env python3

import sys
from Bio import SeqIO

for fn in sys.argv[1:]:
    with open(fn, 'r') as f:
        print('\t<data id="{}" name="alignment">'.format(fn[:-len('_unphased.nex')]))
        for record in SeqIO.parse(f, 'nexus'):
            if record.id.endswith('_1'):

armanbilge

#!/usr/bin/env python3

# The MIT License (MIT)
#
# Copyright (c) 2015 Arman Bilge
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

armanbilge

#/usr/bin/env Rscript

args <- commandArgs(trailingOnly = TRUE)

pdf("boxplots.pdf", width=8,height=20)

par(mfrow=c(5,2))
for (a in args) {
    x <- read.table(a)
    boxplot(x, log = 'y', xlab = "Number of Taxa", main = a)

armanbilge

\documentclass{standalone}

\usepackage{tikz}
\usetikzlibrary{arrows}
\usetikzlibrary{arrows.meta}

\makeatletter
\pgfarrowsdeclare{center*}{center*}
{
  \pgfarrowsleftextend{+-.5\pgflinewidth}

armanbilge

x y z
0.5 1.0 1102.6653073315774
0.7272300105421488 0.8740779740855684 1095.4778163809021
1.1264366494503553 0.4759394735085066 1070.0371428485853
1.1264366494503553 0.4759394735085066 1070.0371428485853
1.116792813277176 0.4760376649851028 1069.7935934823915
1.3596616396957355 0.1133715525159581 1053.7430334714504
1.3596616396957355 0.1133715525159581 1053.7430334714504
1.143913847055679 0.21382193634748284 1051.569214273102
1.0131051618370646 0.07418646571818821 1047.4504891550416

armanbilge

type Node
    label::String
    height::Float64
    parent::Node
    left::Node
    right::Node
end

Node(label::String, height::Float64) = Node(label, height, None, None, None)

armanbilge

using Distributions
using Iterators
using StatsBase

type Particle{T}
    value::T
    weight::Float64
end

Particle{T}(value::T) = Particle(value, 1.0)

armanbilge

import sys
import itertools as it
from collections import Counter

fn = sys.argv[1]

with open(fn) as f:
    N = sum(1 for _ in f)

counts = {}