├── .gitignore ├── LICENSE ├── README.org ├── bin ├── FastqSplitByLength.pl ├── FastqSplitByLength.sh ├── act-blast.sh ├── add-picard ├── aln-maf2seqs.pl ├── aln-maf2stats.pl ├── bcf-alt-consensus ├── bed-gc ├── bed2gff ├── bio2svg ├── blast2bed ├── blast2bed-bash ├── blast2bed-query-bash ├── blast2gff ├── cap3-wrap ├── cluster-ids ├── deiupac ├── dip-sim-gff.pl ├── flye-post ├── fq-fast-stat.pl ├── gb-add-trans ├── gb2faa ├── gb2ffn ├── gb2fna ├── gb2gff ├── gb2gff-seqret ├── gc-window.pl ├── gc.sh ├── gfa2fa ├── gff-clean ├── gff-liftover ├── gff-merge ├── gff-shift ├── gff-strip-fasta ├── gff2bed ├── gff2cds ├── gff2gene ├── hhplot ├── hhplot.R ├── hhr2tsv ├── hmmer-tbl2tsv ├── interleave ├── interleaved-split ├── line2fasta ├── needle-ava ├── r-gamma.R ├── seq-chop ├── seq-circ-restart ├── seq-comp ├── seq-comp-aa ├── seq-error ├── seq-fetch ├── seq-fix-start ├── seq-fq2fa ├── seq-frag ├── seq-gc ├── seq-id-match ├── seq-ids ├── seq-join ├── seq-len ├── seq-len-fai ├── seq-polish ├── seq-reduce ├── seq-rename ├── seq-sample ├── seq-shit ├── seq-shuf ├── seq-split ├── tRNA-extract └── tsv-top ├── data ├── TAIR10_chr1.h1M.fa ├── TAIR10_chr1.h1M.fa.fai ├── TAIR9_GFF3_polymorphisms.h100000.gff ├── TAIR9_chr1.fa ├── TAIR9_chr1.fa.fai ├── at-var.fa ├── bur_0.v7c.1M.sdi ├── hhplot-pfam-32.0.rds ├── ler_0.v7c.1M.sdi ├── seq-circ │ ├── dnaN-uniprot.faa │ ├── dnaN-uniprot.faa.phr │ ├── dnaN-uniprot.faa.pin │ ├── dnaN-uniprot.faa.psq │ ├── rpoB1-uniref50.faa │ ├── rpoB1-uniref50.faa.pdb │ ├── rpoB1-uniref50.faa.phr │ ├── rpoB1-uniref50.faa.pin │ ├── rpoB1-uniref50.faa.pot │ ├── rpoB1-uniref50.faa.psq │ ├── rpoB1-uniref50.faa.ptf │ └── rpoB1-uniref50.faa.pto ├── seq-fix-start │ ├── MED-blast.tsv │ └── dnaN-PF02767_rp75.faa └── wil_2.v7c.1M.sdi ├── etc ├── bio2svg-sample.png ├── bio2svg-sample.svg ├── seq-frag-mp.png └── seq-frag-mp.svg └── t ├── seq-fix-start.t └── seq-fix-start └── dnaN-rc-plus.ffn /.gitignore: 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