diff --git a/tools/emboss_5/emboss_btwisted.xml b/tools/emboss_5/emboss_btwisted.xml
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+ Calculates the twisting in a B-DNA sequence
+ btwisted -sequence $input1 -outfile $out_file1 -auto
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+ You can view the original documentation here_.
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+ .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/btwisted.html
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diff --git a/tools/emboss_5/emboss_cai.xml b/tools/emboss_5/emboss_cai.xml
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+++ b/tools/emboss_5/emboss_cai.xml
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+ CAI codon adaptation index
+ cai -seqall $input1 -outfile $out_file1 -cfile $cfile -auto
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+.. class:: warningmark
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+The input dataset needs to be sequences.
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+-----
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+ You can view the original documentation here_.
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+ .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cai.html
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diff --git a/tools/emboss_5/emboss_cai_custom.xml b/tools/emboss_5/emboss_cai_custom.xml
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index 00000000000..5ff73e8d425
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+++ b/tools/emboss_5/emboss_cai_custom.xml
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+ CAI codon adaptation index using custom codon usage file
+ cai -seqall $input1 -outfile $out_file1 -cfile $input2 -auto
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+.. class:: warningmark
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+The input dataset needs to be sequences.
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+-----
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+ You can view the original documentation here_.
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+ .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cai_custom.html
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diff --git a/tools/emboss_5/emboss_chaos.xml b/tools/emboss_5/emboss_chaos.xml
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index 00000000000..da7eed7c4b4
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+++ b/tools/emboss_5/emboss_chaos.xml
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+ Create a chaos game representation plot for a sequence
+ emboss_single_outputfile_wrapper.pl chaos -sequence $input1 -graph png -goutfile $out_file1 -auto
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+ You can view the original documentation here_.
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+ .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/chaos.html
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