added TOOL_CITATIONS.txt

TOOL_CITATIONS.txt

@@ -0,0 +1,29 @@
+EXTERNAL TOOL CITATIONS:
+Please remember to cite the aligner and tree inference tools that you use
+during the course of a SATe run. The exact citation will depend on what
+tools you choose to use.
+
+Mafft (mafft, disttbfast, dvtditr, pairlocalalign, tbfast):
+    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.