rcedgar

muscle

Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.

urmap

URMAP ultra-fast read mapper

palmscan

newick

Manipulate and generate figures for trees in Newick format

palmdb

Database of virus RdRP barcode sequences

syncmer

Validation of sycnmers compared to minimizers

spades_circular_contigs

Python script to identify circular contigs from SPAdes assembler.

rdrp_tree_experiments

Code, data and results for Muscle5 ensemble experiments on RdRp genus and phylum trees

renomad

Implementation of NOMAD (https://doi.org/10.1101/2022.06.24.497555)

taxxi

Taxonomy cross-validating by identity

circuclust

Clustering and alignment for circular sequences

palm_annot

Scripts, HMMs and search databases for identifying and classifying viral RdRp sequences

jupiter

Generate "Jupiter" plots for circular genomes

balifam

Protein multiple sequence alignment benchmark

qscore

Compares a multiple alignment with a reference and reports accuracy scores.

retree

Python Newick tree format parser and Robinson-Foulds calculator (self-teaching exercise)

simple_paired_read_simulator

A simple paired-read simulator in stand-alone Python2

Baxter_FITs_Microbiome_2016

cmpairs

Parse infernal cmscan tbl file to find pairs of hits to same model on different strands

diamond

Accelerated BLAST compatible local sequence aligner.

dirichlet-cpp

C++ class for Dirichlet distributed random variables

gitignore

A collection of useful .gitignore templates

HelloWorld

A C++ Hello World project, using CMake, and GitHub Actions

regammon

RE-implementation of TD-Gammon

ribozy

Code for identifying candidate ribozyviria sequences

tara_oceans

Data and scripts to reproduce my analysis of Tara Oceans data

tax-credit

A repository for storing code and data related to a systematic comparison of short read taxonomy assignment tools

vcxproj2makefile

Simple python2 script to convert Microsoft Visual Studio C++ project to gcc Makefile

webtest