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.