• aa-code_3to1.sed - substitute 3 letter amino acid abbreviations for 1 letter abbrviations

• parse-dssp.sh - extract secondary structure from PDB files

• exonphaser.sh - add intron-centric phase to a GFF file

• rebase-gff.pl - set all intervals in the GFF as offsets from the first interval

• swap_general.sh - substitute words (with optional pre- and suffixes) using a replacement map

• tozero.pl - replace things nearly equal to zero with zero

• autoslurm.sh - wraps the given command in a slurm file and runs it

• edirect-aliases.sh

• gene-code.sh - print the gene code as a human readable table

• lineage2stratum.pl
• sciname2taxid.sh
• taxid2lineage.pl
• taxid2sciname.pl

The following monstrosities should be murdered and replaced with somethig sane.

• stratify-seqs.sh
• phytable.sh
• fasta2blast_taxidmap.sh

• round.pl
• rplot.R
• sumtab.R
• summarize-gff.awk

• entrez-tools - filters for accessing entrez data

• rentrez-tools - access entrez tools through an R package. To complete this, just wrap some of the functionality described here, however, it is probably better to just directly use the R package.

• retrieve_uniprot_proteomes.py - get all proteomes beneath a given common tree node

• sra2srr.sh - given an SRA id, find the related SRR ids

• sync-bib.sh - recursively extract citations from a tex (or Rnw) file

• gff2cds.pl - use bedtools or bioconductor instead
• rename_fasta.sh - use smof instead