Phylommand - a command line software package for phylogenetics

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. This article is included in the Phylogenetics channel. Martin Ryberg ( ) Corresponding author: [email protected] Ryberg M. How to cite this article: Phylommand a command line software package for phylogenetics [version 1; referees: 2 approved 2016, :2903 (doi: ) with reservations] F1000Research 5 10.12688/f1000research.10446.1 © 2016 Ryberg M. This is an open access article distributed under the terms of the , which Copyright: Creative Commons Attribution Licence permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The author(s) declared that no grants were involved in supporting this work. Grant information: Competing interests: No competing interests were disclosed. 22 Dec 2016, :2903 (doi: ) First published: 5 10.12688/f1000research.10446.1 Referee Status: