基于python的数据分析外文文献_python外文文献.doc

a python Environment for Tree Exploration

Reviewed by Jaime Huerta-Cepas,corresponding author1 Joaqu

í

n Dopazo,2 and Toni Gabald

ó

ncorresponding author1

Abstract

Many

bioinformatics

analyses,

ranging

from

gene

clustering

to

phylogenetics,

produce

hierarchical

trees

as

their

main

result.

These

are

used

to

represent

the

relationships

among

different

biological

entities,

thus

facilitating

their

analysis

and

interpretation.

A

number

of

standalone programs are available that focus on tree visualization or that perform specific analyses

on them. However, such applications are rarely suitable for large-scale surveys, in which a higher

level

of

automation

is

required.

Currently,

many

genome-wide

analyses

rely

on

tree-like

data

representation

and

hence

there

is

a

growing

need

for

scalable

tools

to

handle

tree

structures

at

large scale.

Keywords: Python, spiking neurons, simulation, integrate and fire, teaching, neural networks,

computational neuroscience, software

Background

Here we present the Environment for Tree Exploration (ETE), a python programming toolkit

that

assists

in

the

automated

manipulation,

analysis

and

visualization

of

hierarchical

trees.

ETE

libraries

provide

a

broad

set

of

tree

handling

options

as

well

as

specific

methods

to

analyze

phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis

of

tree

partitions,

has

support

for

the

extended

newick

format,

provides

an

integrated

node

annotation system and permits to link trees to external data such as multiple sequence alignments

or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including

phylogeny-based

orthology

prediction

and

cluster

validation

techniques.

Finally,

ETE's

programmable tree drawing engine can be used to automate the graphical rendering of trees with

customized node-specific visualizations.

Conclusions

ETE

provides

a

complete

set

of

methods

to

manipulate

tree

data

structures

that

extends

current

functionality

in

other

bioinformatic

toolkits

of

a

more

general

purpose.

ETE

is

free

software and can be downloaded from http://ete.cgenomics.org.

Trees

are

commonly

used

to

represent

the

results

of

many

bioinformatics

analyses.

In

particular, such type of binary graphs are ideal to describe the hierarchical relationships among a

variety of biological entities. Some common examples are the evolutionary analysis of molecular

sequences

or

the

clusterization

of

genes

and

proteins

according

to

their

properties.

Besides

the