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clean up repo from alignment testing

I did some work defining thresholds for genome completeness when determining which sequences to include in the full Americas alignment. That meant I had lots of different input fasta files and directories with results files and such. I have the finalized alignment now and so I'm cleaning all the non-used files out to avoid any confusion.
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alliblk committed Oct 16, 2018
1 parent 547676a commit 96a31bca5eba3376238e17158d49cc7865c89c0a
@@ -5,7 +5,7 @@ rule all:
rule files:
input_fasta = "data/publishable-zika-fauna-2018-09-06.fasta",
input_fasta = "data/publishable-zika-fauna-2018-10-15.fasta",
dropped_strains = "config/dropped_strains.txt",
reference = "config/",
colors = "config/colors.tsv",
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