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

SOME BASIC LINUX COMMANDS plus pdf to look into

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