Repositories list

• reCollecTF

  Public
  Streamlined version of the CollecTF database for hosting on GitHub Pages

  JavaScript

  •

  MIT License

  •2•1•0•0•Updated Feb 26, 2026Feb 26, 2026

• reCollecTF_vercel

  Public
  Vercel functions

  TypeScript

  •0•0•0•0•Updated Feb 14, 2026Feb 14, 2026

• Markov_DNA_gen

  Public
  A Markov Model DNA sequence generator to generate pseudo-replicate sequences based on an input sequence

  bioinformaticsstatistical-modelsdna-sequences

  bioinformaticsstatistical-modelsdna-sequences

  Python

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Sep 16, 2025Sep 16, 2025

• ViPhySlim

  Public
  A whole-genome viral phylogeny pipeline

  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 15, 2025Sep 15, 2025

• FLEMINGO

  Public
  A project to generate models of regulated bacterial promoters using genetic programming

  bioinformaticsdnaevolutionary-algorithm+ 1

  bioinformaticsdnaevolutionary-algorithmmotif-discovery

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Aug 2, 2025Aug 2, 2025

• average_entropy

  Public
  Calculates the expected value of the entropy of a uniformly distributed sample of size N over Ω bins (or categories).

  statisticsinformation-theorycomputational-science

  statisticsinformation-theorycomputational-science

  Python

  •0•0•0•0•Updated Apr 21, 2025Apr 21, 2025

• CGA-MD

  Public
  Comparative genomics-assisted motif discovery

  HTML

  •

  MIT License

  •0•1•0•0•Updated Mar 7, 2025Mar 7, 2025

• ViPhy

  Public
  Virus Phylogeny System

  Python

  •0•1•1•0•Updated Feb 15, 2025Feb 15, 2025

• FLEMINGO_test

  Public
  Test set for FLEMINGO on E. coli transcription factors

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

• Info-Theo-of-Composite-Motifs

  Public
  Computational simulations in support of our theoretical work on the information theory of composite motifs

  information-theorymolecular-evolutiontranscriptional-regulation

  information-theorymolecular-evolutiontranscriptional-regulation

  Jupyter Notebook

  •0•2•0•0•Updated Feb 5, 2025Feb 5, 2025

• QD-motifs

  Public
  Evolving TF-binding motifs using quality-diversity algorithms

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jul 1, 2024Jul 1, 2024

• fast_PSSM_search

  Public
  Lookahead implementation of biopython's motif search function

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 25, 2024Jun 25, 2024

• .github

  Public
  Profile repository of the ErillLab organization

  0•0•0•0•Updated Jun 21, 2024Jun 21, 2024

• CAG-MD

  Public
  Comparative genomics-assisted motif discovery

  Python

  •0•0•0•0•Updated Jun 18, 2024Jun 18, 2024

• cgb3EM

  Public
  EM framework for CGB3

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 13, 2024Jun 13, 2024

• PhageReg_CompGen

  Public
  Comparative genomics-based discovery of phage regulatory regions

  GNU General Public License v3.0

  •0•0•0•0•Updated May 30, 2024May 30, 2024

• SPA

  Public
  Code and data used to perform the tAI analysis in deCarvalho et al. (2023)

  bioinformaticsphages

  bioinformaticsphages

  Scheme

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Apr 28, 2024Apr 28, 2024

• cgb3

  Public
  Comparative genomics of prokaryotic transcriptional regulatory networks

  Python

  •

  GNU General Public License v3.0

  •0•2•2•0•Updated Apr 18, 2024Apr 18, 2024

• cgb

  Public
  comparative genomics of transcriptional regulation in Bacteria

  Python

  •2•3•5•2•Updated Jul 6, 2023Jul 6, 2023

• tAI

  Public
  tRNA adaptation index

  Python

  •

  MIT License

  •0•1•0•0•Updated Jun 17, 2023Jun 17, 2023

• PHageR

  Public
  Analysis of host transcriptional regulation on phage genome sequences

  Python

  •

  MIT License

  •0•1•0•0•Updated May 30, 2023May 30, 2023

• frameshift_detector

  Public
  Python

  •0•0•0•0•Updated May 29, 2023May 29, 2023

• SMD

  Public
  Systematic discovery of TF-binding motifs

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated May 1, 2023May 1, 2023

• phylo_seq_gen

  Public
  Pulls sequences of a reference gene from a set of genomes. A MSA of these sequences can be used to construct a phylogeny.

  Python

  •0•0•0•0•Updated Apr 11, 2023Apr 11, 2023

• oprn_consv_calc

  Public
  Aims to determine the structural conservation (i.e. gene order) of an operon within a given taxonomic clade.

  Python

  •1•0•0•0•Updated Apr 11, 2023Apr 11, 2023

• LPEG_phages

  Public
  Code and data for the analysis of TF-binding sites positional entropy in phage genomes, used in Mascolo et al. (2022)

  bioinformaticsphagestranscriptional-regulations

  bioinformaticsphagestranscriptional-regulations

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Feb 26, 2023Feb 26, 2023

• arg_gc

  Public
  Code for the analysis of the antimicrobial resistance gene (ARG) dissemination across the global plasmidome

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 1, 2023Feb 1, 2023

• SOS_Bacteroidetes

  Public
  Code for the analysis of the SOS network in the Bacteroidetes

  Python

  •0•0•0•0•Updated Jan 25, 2023Jan 25, 2023

• pHunter

  Public
  Python second-order approximation to the PromoterHunter code

  bioinformaticspromoterstranscriptional-regulations

  bioinformaticspromoterstranscriptional-regulations

  Python

  •0•1•0•0•Updated Jan 24, 2023Jan 24, 2023

• MD_GP

  Public
  A project to generate models of regulated bacterial promoters using genetic programming

  computational-biologygenetic-programming

  computational-biologygenetic-programming

  Python

  •1•0•0•1•Updated Jan 19, 2023Jan 19, 2023