Sequence Matrix allows you to easily concatenate gene datasets. A spreadsheet-like interface displays what you've assembled so far; TNT, Nexus, FASTA and Mega files can be dragged into the application to add them. Your entire dataset can be exported as TNT or Nexus files.
To find out more, please see our introductory screencast of Sequence Matrix on YouTube. We've also made available a presentation on Sequence Matrix (delivered to the Hennig XXVIII conference in June 2009) and the paper we wrote describing Sequence Matrix in Cladistics.
For users of MacOS X
If you get an "unidentified developer" error, please right-click on the file and select "Open": you should get the some error, but with an "Open" button that allows you to bypass it. Alternatively, you can change your security settings: go to System Preferences on your Mac, click on "Security & Privacy" and go to the "General" tab. If you set "All apps downloaded from:" to "Anywhere", Sequence Matrix should run without any problem.
Here are some reviews of Sequence Matrix we've spotted around the internet.
"It is a real pain combining matrices from different loci, particularly when you have taxa represented in one matrix and not in another. I’ve usually done this by hand and it gets tedious. I recently stumbled across a Java tool that makes this process quite simple: SequenceMatrix." -- The Glor Lab, University of Rochester.
"... the 12 individual gene alignments were concatenated using the software SequenceMatrix v1.7.6 (Vaidya et al., 2011) to create a master alignment of 10,836 bp total, equivalent to roughly 65% of the mtDNA genome." -- Pleistocene diversification of living squirrel monkeys (Saimiri spp.) inferred from complete mitochondrial genome sequences by Kenneth L. Chioua, Luca Pozzia, Jessica W. Lynch Alfaroc and Anthony Di Fiore.
What about Species Identifier?
Species Identifier is no longer being actively maintained. If you want to repeat the analyses in Meier et al, 2006, you can download the latest release.
Problems? Let us know!
If you find any bugs in this or any other release, please report them to us! The source code for this project is available on GitHub.