studies/Chara_Nodal/resources/OligoList.txt

+TABLE 1 Oligonucleotides used in this study 
+
+ID 	Sequence 	Description 
+CBr-CABconsensus-F 	TAATACGACTCACTATAGGGTAGGCCCAGGCGTTGTT 	Northern Blot 
+T7-CBr-CABconsensus-R 	GACCGCCCCAAGTACC 			Northern Blot 
+TruSeq_Sense_nodal 	AATGATACGGCGACCACCGAGATCTACAC-CAAGTGGGACACTCTTTCCCTACACGACGCTCTTCCGATCT 	TruSeq_Sense_primer i5 Barcode 
+TruSeq_Sense_control 	AATGATACGGCGACCACCGAGATCTACAC-AGATTTGGACACTCTTTCCCTACACGACGCTCTTCCGATCT 	TruSeq_Sense_primer i5 Barcode 
+TruSeq_Antisense_nodal 	CAAGCAGAAGACGGCATACGAGAT-TCCGCGAAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT 	TruSeq_Antisense_primer i7 Index 
+TruSeq_Antisense_control 	CAAGCAGAAGACGGCATACGAGAT-TCCGCGAAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT 	TruSeq_Antisense_primer i7 Index 
+
+Note: An added T7 promoter sequence is highlighted in boldface letters.
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workflows/BEASTworkflow.txt

+Input: amino acid sequences aligned with M-coffee 
+BEAST version 2.7.3
+BEAUTi settings:
+   Gamma Site Model, Substitution Model Blosum62
+   Strict Clock - mean clock rate 1.0
+   Prior Yule model, uniform (0,0,infinity), initial [1.0][0.0,infinite]
+   MCMC chain length 1e6, store every 1e4, no pre Burnin, num init attempts 10
+Tracer v1.7.2:
+   validate ESS > 200
+TreeAnnotator:
+   maximum clade credibility tree
+   burnIn 50%
+   posterior probability limit 0.5 (median node heights)
+FigTree v1.4.4:
+   visualisation of generated dendrograms
+     - display tip labels, node labels (posterior)
+   
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