Merge branch 'atlassian_nuke' into 'master'

...des/running_applications/available_software_for_tusker.md

...uides/running_applications/bioinformatics_tools/_index.md

...plications/bioinformatics_tools/alignment_tools/_index.md

...ions/bioinformatics_tools/alignment_tools/blast/_index.md

...ools/alignment_tools/blast/create_local_blast_database.md

...cs_tools/alignment_tools/blast/running_blast_alignment.md

...applications/bioinformatics_tools/alignment_tools/blat.md

...plications/bioinformatics_tools/alignment_tools/bowtie.md

...lications/bioinformatics_tools/alignment_tools/bowtie2.md

...ations/bioinformatics_tools/alignment_tools/bwa/_index.md

...rmatics_tools/alignment_tools/bwa/running_bwa_commands.md

...ons/bioinformatics_tools/alignment_tools/clustal_omega.md

...ns/bioinformatics_tools/alignment_tools/tophat_tophat2.md

...pplications/bioinformatics_tools/biodata_module/_index.md

...ications/bioinformatics_tools/biodata_module/organisms.md

...ns/bioinformatics_tools/data_manipulation_tools/_index.md

...ormatics_tools/data_manipulation_tools/bamtools/_index.md

..._manipulation_tools/bamtools/running_bamtools_commands.md

...ormatics_tools/data_manipulation_tools/samtools/_index.md

..._manipulation_tools/samtools/running_bamtools_commands.md