While the CIPRES portal has become a standard tool for performing RAxML and other phylogenetic analyses, there is certainly an advantage to having a local tool for performing quick phylogenetic analyses. The raxmlGUI tool can be used without internet access, does not have limitations on usage, and does not require the tedious uploading of datasets anytime you need to make a small change. I agree that this tool is great for beginners due to the simplicity of the interface as well as experts for its ease of use for running small or dirty trees.

The authors explain in clear language the basic information needed for phylogenetic analysis and clarify important concepts in ML inference (i.e. superfluity of rooting/outgroup, bipartitions file containing bootstraps). Automatic concatenation of alignments and partitions is a significant innovation as this is often a barrier for new users to perform multi-locus inference. Previously, concatenation would require either a dedicated program like SeaView/MEGA or be performed in command-line/R. The build is another great improvement with this version. The previous version encountered issues with updated OS environments and security/permission conflicts (at least with MacOS).

Following are this reviewer’s suggestions:

As RAxML NG is a new program, it would be helpful to provide more information on what it does and when to use it.

A feature that is lacking in this tool is the ability to estimate evolutionary model/s for different alignments/partitions. This is well-implemented in Bayesian inference programs as well as IQ-tree, a popular alternative to RAxML. This is not the fault of this implementation but of RAxML itself.

Instead of opening alignment files with the system default, it would be great to be able to select a program (i.e. alignment program like AliView) to open specific types of files.

It would be great if we could drop files into the INPUT tab to load alignments instead of clicking and searching. It would also be helpful to be able to upload a partition file instead of manually entering partition information.

When installing the program, I received a message that the previous version of raxmlGUI needed to be replaced. It would be optimal to have the new version be recognized as raxmlGUI 2.0 and separate from the original.

Line 61 – Awkward sentence structure.

Figure 1. – It is not clear on the image where new alignments or partition schemes can be uploaded.

The images given at the end of the manuscript are not listed as Figures and are not cited.