Katelyn

PHANOTATE. PHANOTATE: a gene caller for phages.

PHACTS. A simple program to classify the lifestyle of phages.

prfect. Software to predict the occurence of programmed ribosomal frameshifting in bacterial, phage, and viral genomes

fastpath. A program to find the path through a network of nodes.

genotate. Prokaryotic and phage genome annotation tool

circualign. A tool to align circular genomes on a common feature

RepeatFinder. A python package to quickly find repeats in a DNA sequence

aragorn. tRNA and tmRNA finding

HotKnots. Fast, and best, DNA/RNA folding algorithm

kmeans. A python implementation of the kmeans algorithm that functions as a drop in for sklearn

ReadMapper. ReadMapper is a program that maps sequencing reads to a nucleotide backbone, and then creates a publication quality figure.

bigint. An implementation of a fixed point integer datatype for the C programming language.

MERMAKE. Backend code for the MERFISH+ line of spatial transcriptomic microscopes

goodorfs. Code to classify open reading frames into coding and noncoding

deprekate.github.io. test

rbs-finder. Ribosomal Binding Site Finder

bestblasthit. A small utility to parse blast output and return only the best hit

smith-waterman. A perl implementation of the Smith-Waterman amino acid alignment algorithm

Multivariate-Entropy-Distance. A new non-supervised gene prediction algorithm for bacterial and archaeal genomes

kmer_counter. A fast method for counting rare kmers in nucleotide sequences

parann. Source code for a neural network using back propogation, and in parallel using MPI

genbank. Python code to work with Genbank files