linux

Introduction

Many of the species delimitation tools and auxiliary tools (alignment, phylogenetic inference) are available in easy to use web-services. However, basic knowledge of Linux systems is important in

1. Exploiting the full spectrum of software and their options
2. Handling large files
3. Performing the analyses more efficiently

Tutorial

Open a UNIX terminal window, click on the "Terminal" icon

A terminal window will then appear with a $ prompt, waiting for you to start entering commands:

lkaplipa:~$

To find out where you are execute the pwd command (stands for "print working directory"):

lkaplipa:~$ pwd
/home/lkaplipa

To find out what files and folders are in your directory execute the ls command (stands for "list" from "list directory contents"):

lkaplipa:~$ ls
Documents/ Music/ Analyses/ list.txt 

To create a new directory execute the mkdir command (stands for make directory):

lkaplipa:~$ mkdir linux_tutorial
lkaplipa:~$ ls 
Analyses/ Documents/ linux_tutorial/ Music/ list.txt 

Newick tools

Newick tree definition:

Newick-tools is a software written in C and it is meant to perform a multitude of operations on newick files and visualization of phylogenetic trees. Many of the operation were inspired by small tasks that are essential in species delimitation analyses. It can be particularly useful in handling many and large files and in automating operations (e.g. with simulated data)

Installation

$ git clone https://github.com/xflouris/newick-tools.git

$ cd newick-tools

$ make

Basic functions

show tree features:

print the tree tips of a tree:

$ ./newick-tools --tree_file --output_file --extract_tips

root tree

$ ./newick-tools --tree_file --output_file --root

make tree binary

$ ./newick-tools --tree_file --output_file --make_binary