################################### Frequently Asked Questions for SATé ################################### Q: What does "SATé" mean? A: Simultaneous Alignment and Tree Estimation. Q: How is "SATé" pronounced? A: Sah-tay Q: What formats does SATé use? A: FASTA for sequences, and Phylip for trees (if you are using RAxML, then some of the temporary files that are saved will be in the relaxed phylip format). Q: Where can I find the description of SATé algorithm? A: Please refer to: Liu, K., S. Raghavan, S. Nelesen, C. R. Linder, T. Warnow, "Rapid and Accurate Large-Scale Co-estimation of Sequence Alignments and Phylogenetic Trees", 2009, Science, 324, 1561-1564. for a description of the first variant of the algorithm. The current implementation is most similar to: Liu, K., T.J. Warnow, M.T. Holder, S. Nelesen, J. Yu, A. Stamatakis, and C.R. Linder, "SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees." Systematic Biology. 61(1):90-106. Q: Which alignment programs are included with SATé distribution? A: CLUSTALW 2.0.12 MAFFT 6.717 MUSCLE 3.7 OPAL 1.0.3 PRANK 100311 Q: Which phylogenetic tree reconstruction programs are in SATé distribution? RAxML 7.2.6 FastTree 2.1.4 Q: How to cite SATé software? A: Please cite the two algorithm papers, the software, and the appropriate external tools. ALGORITHM CITATIONS: Liu, K., S. Raghavan, S. Nelesen, C. R. Linder, T. Warnow, 2009. "Rapid and accurate large scale coestimation of sequence alignments and phylogenetic trees." Science, 324(5934):1561-1564, 19 June 2009, doi: 10.1126/science.1171243 Liu, K., T.J. Warnow, M.T. Holder, S. Nelesen, J. Yu, A. Stamatakis, and C.R. Linder. "SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees." Systematic Biology. 61(1):90-106 CITATIONS FOR THE SATé SOFTWARE ITSELF AND ITS DEPENDENCIES: Jiaye Yu, and Mark T. Holder "SATé version VERSION_NUMBER_HERE" from http://phylo.bio.ku.edu/software/sate/sate.html DATE DOWNLOADED. (for version 1.2 or earlier) Jiaye Yu, Mark T. Holder, Jeet Sukumaran, and Siavash Mirarab "SATé version VERSION_NUMBER_HERE" from http://phylo.bio.ku.edu/software/sate/sate.html DATE DOWNLOADED. (for version 1.2.1 to 2.1.0) Jiaye Yu, Mark T. Holder, Jeet Sukumaran, Siavash Mirarab, and Jamie Oaks "SATé version VERSION_NUMBER_HERE" from http://phylo.bio.ku.edu/software/sate/sate.html DATE DOWNLOADED. (for version 2.2.0 or later) Sukumaran, J. and Mark T. Holder. 2010. "DendroPy: A Python library for phylogenetic computing". Bioinformatics 26:1569-1571. (for all SATé versions from this website) EXTERNAL TOOL CITATIONS: Please remember to cite the aligner and tree inference tools that you use during the course of a SATé run. The exact citation will depend on what tools you choose to use. Mafft: See the References section on http://mafft.cbrc.jp/alignment/software/ RAxML: See the Publications section on http://wwwkramer.in.tum.de/exelixis/publications.html Opal: Wheeler, T.J. and Kececioglu, J.D. "Multiple alignment by aligning alignments," Proceedings of the 15th ISCB Conference on Intelligent Systems for Molecular Biology, Bioinformatics 23, i559-i568, 2007. And see http://opal.cs.arizona.edu/ Muscle: Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797. doi:10.1093/nar/gkh340 Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics, (5) 113. doi:10.1186/1471-2105-5-113. See http://www.drive5.com/muscle/ Clustal: See the References section of ftp://ftp.ebi.ac.uk/pub/software/clustalw2/clustalx_help.html Prank: See http://www.ebi.ac.uk/goldman-srv/prank/prank FastTree: Price MN, Dehal PS, Arkin AP. (2010) FastTree 2: Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE 5(3): e9490. doi:10.1371/journal.pone.0009490. Q: What is going on if I see a message like: "SATe ERROR: Error in reading the treefile, probably due to a name in the tree that does not match the names in the input sequence files. SATe ERROR: SATe is exiting because of an error: 'Taxon "Urochroa_bougueri" not in TaxonSet, and cannot be created because TaxonSet is immutable' "? A: This indicates that the names of the sequences (aka 'taxa') in the tree did not match the names found in the FASTA file. Check the FASTA file for the name that appears in single quotes in the error message (this is a name that was found in the tree).