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Assembling the Tree of Life: Orchidaceae ONCIDIINAE (ORCHIDACEAE) University of Florida Herbarium Home

This study expands our previous work on subtribes Maxillariinae, Oncidiinae, Zygopetalinae, and Stanhopeinae.


DOWNLOADS

The *.nex files can be downloaded for you to examine on your computer. These files are available for viewing by downloading them (search for Oncidiinae) from the Dryad digital repository site (or just click on the file name below, but the files you download from here will not be aligned) and will work only on a late model computer with lots of RAM. If you are using a MAC, then you can examine the matrices using color fonts, but you need to first extract or expand the Colorfonts.sea.bin file and then put it in your SYSTEM folder in the FONTS folder on your MAC. You need the latest version of PAUP* (- available from Sinaeur Associates - ) to examine or run these files, but this is the only good way for you to see our data matrices. We assume you know something about cladistics and molecular systematics, as well as how to execute a NEXUS file and run PAUP* analyses.

FreeMind is available free for download from the FreeMind web site. If it does not run on your computer, please let me know, stating the browser and operating system you are using.

Andrew Rambaut's excellent program Se-Al is a program for creating alignments in color. It is available FREE from the web site, it only runs on MAC's, but Se-Al will not run on Mac OS X 10.7. Sorry PC users, but he has no plans to make it available for PC's. There might be programs out there that make color fonts for PC's, but I am not aware of any that are as good as Se-Al. The only program that comes close (as far as I know) is SeaView, a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView is available and free for PC's and MAC's, as well as for 32-bit Linux on x86, 64-bit Linux on x86_64, and Solaris on SPARC. It is not as user friendly as Se-Al, but it does do alignments with Muscle and Clustal Omega and the alignments are in color.
The file Oncid7gene.nex is a combined large data matrix of 736 samples (representing approximately 600 species) and 8,020 characters. This will allow you to generate a cladogram based on nrITS, trnH-psbA, 5'ycf1, 3'ycf1, and matK.

The file Oncid_COMB.nex is a matrix of ITS, trnH-psbA, 3'ycf1, 5'ycf1, matK, rbcL, and psaB for 122 taxa and 10,023 characters. It is set up so you can analyze for any one region, or all of them combined. This smaller, restricted taxon analysis included several relatively conserved plastid genes (rbcL, psaB) with the goal of providing increased resolution and support for the spine of the tree.

The file Colorfonts.sea.bin contains the color font file you will need to really work with the data matrix and see what's going on.


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Page last updated: 4 December 2013