c5shen Goto Github PK

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

cm_pipeline

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

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

cs125fall20quizprep

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

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

emma

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

gpu-blast-plus

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

hmmerge

kmsortfile

k-means clustering sorting to heatmap display

learnmsa

Learning and Aligning Large Protein Families (MSA-HMM)

llm.c

LLM training in simple, raw C/CUDA

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.

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.

witch

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