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Updated: Aug 12, 2025

A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
Concatenator, a user-friendly program to concatenate DNA sequences, implementing graphical user interfaces for MAFFT
Miguel Vences1, Stefanos Patmanidis2, Vladimir Kharchev1
1Division of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany.
Motivation:
Phylogenetic and phylogenomic analyses require multi-gene input files in different formats, but there are few user-friendly programs facilitating the workflow of combining, concatenating or separating, aligning and exploring multi-gene datasets.
Results:
We present Concatenator, a user-friendly GUI-driven program that accepts single-marker and multi-marker DNA sequences in different input formats, including Fasta, Phylip and Nexus, and that outputs concatenated sequences as single-marker or multi-marker Fasta, interleaved nexus or Phylip files, including command files for downstream model selection in IQ-TREE. It includes the option to (re)align markers with MAFFT and produces exploratory trees with FastTree. Although tailored for medium-sized phylogenetic projects, Concatenator is able to process phylogenomic datasets of up to 30 000 markers.
Availability And Implementation:
Concatenator is written in Python, with C extensions for MAFFT and FastTree. Compiled stand-alone executables of Concatenator for MS Windows and Mac OS along with a detailed manual can be downloaded from www.itaxotools.org; the source code is openly available on GitHub (https://github.com/iTaxoTools/ConcatenatorGui).
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