Phylommand - a command line software package for phylogenetics

Martin Ryberg

doi:10.12688/f1000research.10446.1

Abstract

Phylogenetics is an intrinsic part of many analyses in evolutionary biology and ecology, and as the amount of data available for these analyses is increasing rapidly the need for automated pipelines to deal with the data also increases. Phylommand is a package of four programs to create, manipulate, and/or analyze phylogenetic trees or pairwise alignments. It is built to be easily implemented in software workflows, both directly on the command prompt, and executed using scripts. Inputs can be taken from standard input or a file, and the behavior of the programs can be changed through switches. By using standard file formats for phylogenetic analyses, such as newick, nexus, phylip, and fasta, phylommand is widely compatible with other software.

Highlights

The improvement of high throughput sequencing methods, and the ability to produce more and/or longer reads at a cheaper price have allowed the use of these data in new areas of research (Ellison et al, 2011; Jumpponen & Jones, 2009; Lemmon et al, 2012)
Phylommand is a package of four software - treebender, treeator, contree, and pairalign - with capabilities in manipulation and analyses of phylogenetic trees
Similar to the Newick utilities software suit (Junier & Zdobnov, 2010), that act on phylogenetic trees, the phylommand programs are designed to be used on the command line, without the overhead from a graphical interface

Summary

Introduction

The improvement of high throughput sequencing methods, and the ability to produce more and/or longer reads at a cheaper price have allowed the use of these data in new areas of research (Ellison et al, 2011; Jumpponen & Jones, 2009; Lemmon et al, 2012). More or less, automated software pipelines are often an intrinsic part in the development of ways to process and analyze data for new types of research questions. Phylommand is a package of four software - treebender, treeator, contree, and pairalign - with capabilities in manipulation and analyses of phylogenetic trees. In addition there are functions, such as calculating decisiveness (Sanderson et al, 2010), MAD scores (Smith et al, 2009), and matrix representation of trees, for use in supermatrix and supertree pipelines. Similar to the Newick utilities software suit (Junier & Zdobnov, 2010), that act on phylogenetic trees, the phylommand programs are designed to be used on the command line, without the overhead from a graphical interface.

Methods

Conclusion