Submitted by: Anupama (0041109)
Set 1 FootPrinter output. Sequence of interest are – GAGCTG / AAGCTG, TTCCAG / TTCTTT, GAAAGA / ATAAGA. None of these match the output from Clustal W or Dialign.
FootPrinter command line
FootPrinter ../COG0050.txt ../COG0050Tree.txt -sequence_type upstream -size 6 -max_mutations 10 -max_mutations_per_branch 2
Set 2 FootPrinter output. Sequence of interest are – CATTGA. This matches 5 characters in ACATTG found by DiAlign.
FootPrinter command line
FootPrinter ../COG0480.txt ../COG0480Tree.txt -sequence_type upstream -size 6 -max_mutations 2 -max_mutations_per_branch 1 -subregion_size 50 -position_change_cost 1
Set 3 FootPrinter output. Sequence of interest are – CGTTCA. This matches 4 characters in CGCCGTT produced by Clustal W. and also 4 characters in GCCGTT produced by DiAlign.
FootPrinter command line
FootPrinter ../COG0173.txt ../COG0173Tree.txt -sequence_type upstream -size 6 -max_mutations 2 -max_mutations_per_branch 1 -subregion_size 50 -position_change_cost 1 -compute_branch_lengths -losses universal6.config -loss_cost 1