David Pattinson davipatti

Selecting dissimilar leaves in a phylogenetic tree

To select N leaves.

- Pick a leaf at random. Add it to a selected list.

While N &lt; len(selected):

Notes from installing Ubuntu 18.04 on a Lenovo ThinkPad X1 Extreme, with nvidia graphics.

Entity	Code	Year	Life expectancy (Clio-Infra up to 1949; UN Population Division for 1950 to 2015)
Afghanistan	AFG	1950	27.537001
Afghanistan	AFG	1951	27.809999
Afghanistan	AFG	1952	28.35
Afghanistan	AFG	1953	28.879999
Afghanistan	AFG	1954	29.399
Afghanistan	AFG	1955	29.907
Afghanistan	AFG	1956	30.403999
Afghanistan	AFG	1957	30.891001
Afghanistan	AFG	1958	31.367001

	#!/usr/bin/env python3

	"""2019-04-10 David Pattinson

	Plot the parameter samples from a MrBayes run.

	- Run this script in a directory that contains *.p files, or that contains
	subdirectories (however deep) that contain *.p files.
	- Any .p files in the same directory will be plotted on the same trace.
	E.g. if HA.run1.p and HA.run2.p are in the same directory, their traces

	#!/usr/bin/env python3
	import sys
	from itertools import groupby
	lines = sorted(map(lambda l: l.rstrip(), sys.stdin.readlines()))
	counts = ((len(list(group)), line) for line, group in groupby(lines))
	for count, line in sorted(counts, key=lambda x: x[0]):
	print("{:7d} {}".format(count, line))

	from sense_hat import SenseHat
	from functools import reduce
	from operator import add
	import random

	i = 51, 160, 44
	o = 178, 223, 138
	rows = 8
	cols = 8

	def attachX(tree):
	for node in tree.preorder_node_iter():
	if node.parent_node is None:
	node.x = 0
	else:
	node.x = node.edge.length + node.parent_node.x

	def attatchYLeaves(tree):
	for y, node in enumerate(tree.leaf_node_iter()):
	node.y = y

	library(geometry)
	library(plotly)

	xyz <- c("x", "y", "z")

	convexHull <- function(group) {

	# I forget whata he name of the variable containing
	# the data.frame is, and the name of the column
	# that contains the groups