c5shen

WITCH

WITCH is a multiple sequence alignment method that uses multiple weighted HMMs to align unaligned sequences and find consensuses.

EMMA

an ensemble usage of MAFFT-linsi --add on large datasets

CS125Fall20QuizPrep

A repo where I will post questions that summarize prior week's contents to help students prepare for the next week's quiz.

GPU-BLAST-plus

A class project for CS508 from UIUC to implement the classic BLAST algorithm using different GPU computing techniques.

VireTap

A 03-713 Bioinformatics Practicum project. It focuses on virus transcriptome detection of a given diseased model (i.e. human cancer) using RNA-seq data, and in the future, some further analyses including SNP analysis etc.

kmSortFile

k-means clustering sorting to heatmap display

cm_pipeline

Pipeline that uses an improved version of CM for generating well-connected clusters

ATMerger

A standalone alignment merging tool that utilizes transitivity that merges a set of overlapping alignments. The original implementation comes from PASTA and UPP (see README).

BSCAMPP_code

New Code for EPA-ng-BSCAMPP

ColabFold

Copy of colabfold. Adding options to realign the retrieved sequences from MMSeqs2

CommonLibSSE-NG

This is a reverse engineered library for Skyrim Special Edition and Skyrim VR.

connectivity-modifier

better community detection through small cuts

constrained-INC

A copy of constrained-INC (INC) from steven-le-thien

contrained-MAGUS

Graph Clustering Merger

crucible

CS598FinalProject

Git repo for the CS598 final project. This is a simple modification to the ILP version of PhISCS, where we allow the model to handle ISA (infinite site assumption) violations implicitly.

DEPP

HMMerge

learnMSA

Learning and Aligning Large Protein Families (MSA-HMM)

MAGUS-legacy

A legacy version of MAGUS that I will personally work on

my-deep-learning-collection

A collection of deep learning implementations, including MLP, CNN, RNN. Additionally, a new CNN approach for solving PDEs are provided (GACNN).

njmerge

A tool for divide-and-conquer tree estimation via a shared distance matrix

Novelty

Codes for computing novelty indicators.

OrthoFinder

Phylogenetic orthology inference for comparative genomics

PLUSplacer

sepp

Ensemble of HMM methods (SEPP, TIPP, UPP)

soulsy

A minimal Souls-like HUD for Skyrim AE & SE. SKSE plugin.