Using MSAJ

MSAJ is a single window application, when you initialize it you will see a few icons, a text box and a disabled button.

It can join Multi Sequence Alignments (MSA) from FASTA and NEXUS file formats. These MSAs must have the same number of taxa with the exact same name accross all files, but they do not have to be in the same order.

To import files use the open files or the open folder buttons. The Open Files button will allow you to select more than one file, the Open Folder will allow you to select a single directory that must contain your alignment files to import.

If the files do not contain exact matches of taxa names or are corrupted in any way, MSAJ will not join the MSAs, once it will not be capable of matching taxa among files. If this happens an error will be shown in the text box.

Some error messages may help you identify the issues and correct them.

If everything is as expected and the data was imported from the MSAs correctly, MSAJ will present you a small summary of the imported data.

At this point the Merge Button will become clickable, if you click it a window asking you to save the merged file will pop up. Enter a file name and choose a directory to save the file. Once done, the file will be saved and MSAJ will show a few more information in the text box.

MSAJ saves your files in NEXUS format only. This format suports more information about your alignment than other formats, so MSAJ can save inside the NEXUS file the character sets, in cause you need that information for partitioned analysis.

The names of the sets are based upon your files names, but you can edit it at will. Just avoid blank spaces and special characters.