RAxML Workbench

Version: 1.0

(c) Exelixis Lab.

Contact

• Denis.Krompass@campus.lmu.de

RAxML-EPA:

• S.A. Berger, A. Stamatakis, Evolutionary Placement of Short Sequence Reads. arXiv:0911.2852v1 [q-bio.GN](2009)

RAxML:

• A. Stamatakis, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22 (2006) btl446

Archaeopteryx Treeviewer:

• Han, Mira V.; Zmasek, Christian M. (2009). phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics (United Kingdom: BioMed Central) 10: 356. doi:10.1186/1471-2105-10-356. http://www.biomedcentral.com/1471-2105/10/356
• Zmasek, Christian M.; Eddy, Sean R. (2001). ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics (United Kingdom: Oxford Journals) 17 (4): 383–384. http://bioinformatics.oxfordjournals.org/cgi/reprint/17/4/383

EDPL:

• Frederick A Matsen, Robin B Kodner and E Virginia Armbrust, pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. arXiv:1003.5943v1 [q-bio.PE]

Hmmer:

• S. R. Eddy., A New Generation of Homology Search Tools Based on Probabilistic Inference. Genome Inform., 23:205-211, 2009.

uclust:

• http://www.drive5.com/uclust