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--- a/Example/Example-without-alignment-cutting/run-example.sh
+++ b/Example/Example-without-alignment-cutting/run-example.sh
@@ -1 +1,2 @@
-../../BaitFisher-v1.2.7 parameter.txt 1> console_output 2> console_error_output
+#!/bin/sh
+BaitFisher parameter.txt 1> console_output 2> console_error_output
--- a/Example/Example-with-alignment-cutting-and-required-taxa/run-example.sh
+++ b/Example/Example-with-alignment-cutting-and-required-taxa/run-example.sh
@@ -1,2 +1,3 @@
-BaitFisher-v1.2.7 parameterfile.txt &> runner.log
+#!/bin/sh
+BaitFisher parameterfile.txt &> runner.log
--- a/Example/Example-without-alignment-cutting/BaitFilter-analysis/run-BaitFilter.sh
+++ b/Example/Example-without-alignment-cutting/BaitFilter-analysis/run-BaitFilter.sh
@@ -1,6 +1,7 @@
-BaitFilter-v1.0.6 -m ab -i ../BaitFisher-results/loci_baits.txt -o baits_filtered_best-in-alignment_minNumBaits.txt 1> console_o_filter_bestBaits 2> console_e_filter_bestBaits
-BaitFilter-v1.0.6 -m as -i ../BaitFisher-results/loci_baits.txt -o baits_filtered_best-in-alignment_maxNumSeq.txt 1> console_o_filter_bestSeqs 2> console_e_filter_bestSeqs
+#!/bin/sh
+BaitFilter -m ab -i ../BaitFisher-results/loci_baits.txt -o baits_filtered_best-in-alignment_minNumBaits.txt 1> console_o_filter_bestBaits 2> console_e_filter_bestBaits
+BaitFilter -m as -i ../BaitFisher-results/loci_baits.txt -o baits_filtered_best-in-alignment_maxNumSeq.txt 1> console_o_filter_bestSeqs 2> console_e_filter_bestSeqs
## Produce bait file that can be uploaded at a bait producing company. So war all companies accepted the file produced with the following command.
-BaitFilter-v1.0.6 -c Agilent-Germany -i baits_filtered_best-in-alignment_maxNumSeq.txt -o Final_baits_filtered_best-in-alignment_maxNumSeq.txt --ID-prefix My-project-name- 1> conversion_maxNumSeq.o 2> conversion_maxNumSeq.e
-BaitFilter-v1.0.6 -c Agilent-Germany -i baits_filtered_best-in-alignment_minNumBaits.txt -o Final_baits_filtered_best-in-alignment_minNumBaits.txt --ID-prefix My-project-name- 1> conversion_minNumBaits.o 2> conversion_minNumBaits.e
\ No newline at end of file
+BaitFilter -c Agilent-Germany -i baits_filtered_best-in-alignment_maxNumSeq.txt -o Final_baits_filtered_best-in-alignment_maxNumSeq.txt --ID-prefix My-project-name- 1> conversion_maxNumSeq.o 2> conversion_maxNumSeq.e
+BaitFilter -c Agilent-Germany -i baits_filtered_best-in-alignment_minNumBaits.txt -o Final_baits_filtered_best-in-alignment_minNumBaits.txt --ID-prefix My-project-name- 1> conversion_minNumBaits.o 2> conversion_minNumBaits.e
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