├── Install_bioSyntax.sh ├── LICENSE.md ├── README.md ├── bioSyntax_talk.pptm ├── docs ├── .sass-cache │ └── 68710e094d770af080a52dddf9b6dabfc7ddb404 │ │ ├── jekyll-theme-slate.scssc │ │ └── rouge-github.scssc ├── CNAME ├── Gemfile ├── Gemfile.lock ├── _config.yml ├── _layouts │ └── default.html ├── _sass │ ├── jekyll-theme-slate.scss │ └── rouge-github.scss ├── _site │ ├── CNAME │ ├── Gemfile │ ├── Gemfile.lock │ ├── assets │ │ ├── css │ │ │ └── style.css │ │ └── images │ │ │ ├── FastaBanner.png │ │ │ ├── bg_hr.png │ │ │ ├── bioSyntax_logo.png │ │ │ ├── blacktocat.png │ │ │ ├── blacktocat2.png │ │ │ ├── hackseq_logo_sq_inv_Solid.png │ │ │ ├── hackseq_logo_sq_inv_icon.png │ │ │ ├── icon_download.png │ │ │ ├── sam-less.png │ │ │ ├── sam-less_command.png │ │ │ └── sprite_download.png │ ├── index.md │ └── script │ │ ├── bootstrap │ │ ├── cibuild │ │ └── release ├── assets │ ├── css │ │ └── style.scss │ └── images │ │ ├── FastaBanner.png │ │ ├── bg_hr.png │ │ ├── bioSyntax_logo.png │ │ ├── blacktocat.png │ │ ├── blacktocat2.png │ │ ├── hackseq_logo_sq_inv_Solid.png │ │ ├── hackseq_logo_sq_inv_icon.png │ │ ├── icon_download.png │ │ ├── sam-less-small.gif │ │ ├── sam-less.png │ │ ├── sam-less_2.png │ │ ├── sam-less_command.gif │ │ ├── sam-less_command.png │ │ └── sprite_download.png ├── collaborate.md ├── formats.md ├── index.md ├── install.md ├── manual.md └── script │ ├── bootstrap │ ├── cibuild │ └── release ├── examples ├── annot │ ├── test.bedpe │ ├── test1.bed │ ├── test1.wig │ ├── test2.wig │ ├── test_cufflinks.gtf │ ├── test_gencode.gtf │ └── test_refseqUCSC.gtf ├── nt-seq │ ├── bioSyntax.fa │ ├── test1.fa │ ├── test1.fq │ ├── test1_prot.faa │ ├── test2.fa │ ├── test2.fq │ ├── test2.fq.gz │ ├── test3.fasta │ ├── test_alignment1.clustal │ ├── test_alignment1.mfa │ ├── test_alignment1.phylip │ ├── test_alignment2.clustal │ ├── test_gcContent.fa │ ├── test_gcContent_randomer.fa │ └── test_gcContent_randomer_gradient.fa ├── pdb │ ├── pdbx.link │ ├── test.pdb │ ├── test2.pdb │ └── test2.pdbx ├── sam │ ├── mario.sam │ ├── test.fa.fai │ ├── test.flagstat │ ├── test1.sam │ ├── test2.sam │ └── test4_large.sam └── vcf │ ├── test.vcf │ ├── test_1000genomes.vcf.gz │ └── test_dbSNP.vcf ├── syntax ├── archive │ └── bioSyntax_sublime_v171022.zip ├── bioSyntax_sublime_RELEASE.zip ├── gedit │ ├── bed.lang │ ├── bioKate.xml │ ├── bioSyntax.lang │ ├── bioSyntax.xml │ ├── clustal.lang │ ├── faidx.lang │ ├── fasta-clustal.lang │ ├── fasta-hc.lang │ ├── fasta-hydrophobicity.lang │ ├── fasta-taylor.lang │ ├── fasta-zappo.lang │ ├── fasta.lang │ ├── fastq.lang │ ├── gtf.lang │ ├── quickInstall_unix.sh │ ├── sam.lang │ ├── vcf.lang │ └── wig.lang ├── less │ ├── bed.lang │ ├── bioSyntax-vcf.outlang │ ├── bioSyntax.outlang │ ├── bp_append.txt │ ├── clustal.lang │ ├── faidx.lang │ ├── fasta.lang │ ├── fasta.style │ ├── fastq.lang │ ├── flagstat.lang │ ├── gtf.lang │ ├── pdb.lang │ ├── pdb.style │ ├── quickInstall.sh │ ├── rc_append.txt │ ├── sam.lang │ ├── sam.style │ ├── src-hilite-lesspipe_BIO.sh │ ├── vcf.lang │ └── vcf.style ├── sublime │ ├── Color Scheme - bioSyntax.sublime-package │ ├── bed.sublime-syntax │ ├── clustal.sublime-syntax │ ├── faidx.sublime-syntax │ ├── fasta-clustal.sublime-syntax │ ├── fasta-hc.sublime-syntax │ ├── fasta-hydro.sublime-syntax │ ├── fasta-taylor.sublime-syntax │ ├── fasta-zappo.sublime-syntax │ ├── fasta.sublime-syntax │ ├── fastq.sublime-syntax │ ├── flagstat.sublime-syntax │ ├── gtf.sublime-syntax │ ├── pdb.sublime-syntax │ ├── sam.sublime-syntax │ ├── vcf.sublime-syntax │ └── wig.sublime-syntax └── vim │ ├── bed.vim │ ├── clustal.vim │ ├── colors │ └── bioSyntax.vim │ ├── faidx.vim │ ├── fasta-hc.vim │ ├── fasta.vim │ ├── fastq.vim │ ├── ftdetect │ ├── bed.vim │ ├── clustal.vim │ ├── faidx.vim │ ├── fasta.vim │ ├── fastq.vim │ ├── gtf.vim │ ├── pdb.vim │ ├── sam.vim │ └── vcf.vim │ ├── gtf.vim │ ├── pdb.vim │ ├── quickInstall_unix.sh │ ├── sam.vim │ └── vcf.vim └── theme ├── gedit ├── bioKate.xml └── 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