ErillLab/ViPhy

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Python
Created about 4 years ago
Updated over 1 year ago

ErillLab/ViPhy

ErillLab

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Virus Phylogeny System

collectf

CollecTF database implementation

gpu_pssm

A GPU-based implementation of sliding window PSSM scoring.

cgb

comparative genomics of transcriptional regulation in Bacteria

Markov_DNA_gen

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

tAI

tRNA adaptation index

FLEMINGO

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

SPA

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

vibrio-biofilm-formation

In silico analysis of promoter architecture for biofilm formation genes involved in Vibrio cholerae

pHunter

Python second-order approximation to the PromoterHunter code

control_seq_gen

Generates control sequences for motif analysis. Goal is to maintain the statistical parameters of the input sequences (i.e. nucleotide composition) without recapitulating the sites of interest.

LPEG_phages

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