niemasd

TreeSwift

TreeSwift: Fast tree module for Python 3

TreeCluster

Efficient phylogenetic clustering of viral sequences

ViralMSA

Reference-guided multiple sequence alignment of viral genomes

ViralConsensus

Fast viral consensus genome reconstruction

teaching

My teaching resources

MESS

MESS: Moshiri Exam Similarity Score

SamBamViz

Tool for generating useful visualizations from a SAM/BAM file

FAVITES-Lite

FAVITES-Lite: A lightweight framework for viral transmission and evolution simulation

SD-COVID-Sequencing

My scripts/notes from the San Diego COVID sequencing effort

curriculum-vitae

Niema Moshiri's Curriculum Vitae (CV)

FAVITES-ABM-HIV-SD-Lite

A simplified simulation pipeline specifically for ABM-HIV SD

Game-Saves

My backups of game saves

BISB-Website

Stuff related to my work in updating the UCSD BISB program website

cawlign-bealign-benchmark

Benchmark of cawlign and bealign

How-to-Teach-Online

An online training module to provide instructors guidance in developing and offering fully-online and hybrid courses

Hyper-Gen

HyGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors

NiemaGraphGen

Niema's C++ implementations of graph generators

niemasd.github.io

Niema Moshiri's website

Big-Ass-Data-Broker-Opt-Out-List

biowasm

WebAssembly modules for genomics

cawlign

hivtrace-true-append

Code related to HIV-TRACE "True Append"

mister_unstable_updater_scripts

Niema-Twitter-Blocks

An archive of Niema's Twitter blocks

Paper_emergence_time_SARS-CoV-2

This repository contains the fasta files necessary to reproduce the analysis

PicoSync

Sync combiner and C-Sync fixer on the Raspberry Pi Pico

Plex-Library-Viewer

Python tool that uses the Plex API to view details about a Plex library

tn93

TN93 fast distance calculator

Unstable_Folder_MiSTer

Unstable nightlies

Ys-I-II-Chronicles-Plus-Save-Editor

Save editor for Ys I & II Chronicles+