isaacs

# Hello, and welcome to makefile basics.
#
# You will learn why `make` is so great, and why, despite its "weird" syntax,
# it is actually a highly expressive, efficient, and powerful way to build
# programs.
#
# Once you're done here, go to
# http://www.gnu.org/software/make/manual/make.html
# to learn SOOOO much more.

sigoden

wget -O /tmp/YaHei.Consolas.1.12.zip https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/uigroupcode/YaHei.Consolas.1.12.zip
unzip /tmp/YaHei.Consolas.1.12.zip
sudo mkdir -p /usr/share/fonts/consolas
sudo mv YaHei.Consolas.1.12.ttf /usr/share/fonts/consolas/
sudo chmod 644 /usr/share/fonts/consolas/YaHei.Consolas.1.12.ttf
cd /usr/share/fonts/consolas
sudo mkfontscale && sudo mkfontdir && sudo fc-cache -fv

johnatasjmo

setwd("~/rProgramming")
files.sources = list.files()
sapply(files.sources, source)

josephwb

## written by:
# Joseph W. Brown (josephwb, @j0sephwb)
# Klaus Schliep (KlausVigo, @Klaus_Schlp)
get_mrca_fast <- function(phy, tip) {
    if (!inherits(phy, "phylo")) {
        stop('object "phy" is not of class "phylo"');
    }
    if (length(tip) < 2) {
        return(NULL);
    }

josephwb

// g++ -Wall getlineSafe.cpp -o getlineSafe -O

#include <string.h>
#include <iostream>
#include <fstream>
#include <cstdlib>

std::istream& getlineSafe(std::istream& is, std::string& t) {
    t.clear();

josephwb

# extract subtree induced from a set of tips
subtree.induced <- function (phy, tip) {
    if (!inherits(phy, "phylo")) {
        stop("object \"phy\" is not of class \"phylo\"");
    }
    Ntip <- length(phy$tip.label);
    
    # convert to indices if strings passed in
    if (is.character(tip)) {
        idx <- match(tip, phy$tip.label);

josephwb

require(phangorn);

# check the monophyletic status of every genus in the tree `phy`
check_genus_monophyly <- function (phy) {
    # get genera. assumes form: Genus_species_whatever
    gens <- sort(unique(sub("_.*", "", phy$tip.label)));
    n <- length(gens);
    cat("Checking ", n, " genera for monophyly status.\n", sep="");
    # the number of descendant tips of the MRCA. preallocate for monotypic genera
    ndec <- rep(1, n);

josephwb

#!/bin/bash

# report files greater than some size (default 100 MB)
# does so recursively starting at some dir (default pwd)

# to make executable, do:
# chmod +x find_large_files.sh

print_help () {
    echo "Recursively find all files larger than some size"

roblanf

# Create a scatterplot with any species as the data points.
# To choose your species, go here: http://phylopic.org/ , then enter the name of the spp you want. Click on the image and click 'thumbnail', click on the picture, and then copy the link in the address bar of your browser. It should end with 'thumb.png' Paste it in place of the link below.

library(TeachingDemos)
library(png)

# Paste a link to a png of your favourite animal here. This will be an aardvarkplot. Make sure it ends with .thumb.png.
# If it doesn't end with .thumb.png reread the instructions above and try again.
link = "http://phylopic.org/assets/images/submissions/cfee2dca-3767-46b8-8d03-bd8f46e79e9e.thumb.png"

carlosp420

#!/usr/bin/perl -w

#this script converts a tree ouput from TNT to NEXUS (1 tree per file)
# Carlos Peña 2011-03-16

use strict;
use Bio::TreeIO;
        my $usage = "script.pl INFILE OUTFILE\n";
        my $infile = shift or die $usage;
        my $outfile = shift or die $usage;