Sequence Matrix

Sequence Matrix is a Java-based software application that facilitates a user-friendly environment for analyzing phylogenetic data matrices and assembling them with multiple genes. It features sample files and lets you export sequences to various formats.

Provided that you have Java on your computer, it's not necessary to install anything else. You can simply drop the program files anywhere on the disk or on a USB flash drive and directly run the executable Jar file on any computer with Java. More importantly, unlike most installers, it shouldn't make any changes to the Windows registry.

The GUI is based on a standard window with a well-structured layout, where you can use samples and import sequences from FAS-formatted files, analyze columns with taxons, total lengths and number of charsets, create outgroups, and delete any taxon. Sequences can be sorted by name, species epithet, number of character sets, or total length, depending on your preferences.

It's possible to track down distances in all genes by specifying a range, view pairwise distances, export the table as a tab-delimited file, as well as to export sequences as TNT or NEXUS. Alternatively, sequences can be split into multiple files for each column, as well as saved for RAxML analysis on CIPRES.

No error dialogs popped up in our tests, and the software utility didn't cause the operating system to hang or crash. It didn't put a strain on the overall performance of the machine, thanks to the fact that it needed low CPU and RAM to work properly.

On the other hand, the interface is a bit rusty, and the options are not intuitive for less experienced users. Nevertheless, you can test Sequence Matrix for yourself, since it's free to use.