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balifam

Protein multiple sequence alignment benchmark

baxter_fits_microbiome_2016

circuclust

Clustering and alignment for circular sequences

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

jupiter

Generate "Jupiter" plots for circular genomes

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.

newick

Manipulate and generate figures for trees in Newick format

palm_annot

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

palmdb

Database of virus RdRP barcode sequences

palmscan

qscore

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

rdrp_tree_experiments

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

regammon

RE-implementation of TD-Gammon

renomad

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

reseek

Protein structure alignment and search algorithm

retree

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

ribozy

Code for identifying candidate ribozyviria sequences

simple_paired_read_simulator

A simple paired-read simulator in stand-alone Python2

spades_circular_contigs

Python script to identify circular contigs from SPAdes assembler.

syncmer

Validation of sycnmers compared to minimizers

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

taxxi

Taxonomy cross-validating by identity

urmap

URMAP ultra-fast read mapper

usearch12_documentation

Documentation for USEARCH v12

vcxproj2makefile

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