File	README.md
Lecture	Advanced Bioinformatics 1
Professor	Martin Steinegger (martin.steinegger@snu.ac.kr)
TA	Sukhwan Park (pskvins@snu.ac.kr)
Last Modified	2023-09-06 13:59:05 -0700

Advanced Bioinformatics 1

The paper pool for Advanced Bioinformatics 2021

Annotation

1. Augustus paper, github
2. BRAKER2 paper, github
3. Prodigal paper, github

Genome comparison

1. mummer1-4 paper, github
2. mash paper, github
3. FastANI paper, github

Multiple sequence alignment (MSA)

1. clustalomega paper, github, homepage
2. Muscle5 paper, github, homepage
3. Progressive Cactus paper1, paper2, github

Homology search

1. mmseqs2 paper, github
2. Diamond1+2 paper1, paper2, github
3. HHblits paper1, paper2, github
4. Foldseek paper, github
5. tm-align paper, website

Transcript

1. kallisto paper, github, homepage
2. salmon paper, github, homepage
3. Oases paper, github
4. CellChat paper, github
5. rMATs paper, github

Metagenomics

1. kraken-uniq paper, github
2. HUMAnN2 paper, github, homepage
3. Kaiju paper, github, homepage

Phylogenetics

1. raxml paper, github, homepage
2. iqtree paper, github, homepage
3. MrBayes paper, homepage

RNA structure prediction

1. viennarna paper, github, homepage
2. R-scape paper, software, homepage
3. UFold paper, github

Protein structure

1. RoseTTAFold paper, github
2. gromacs paper, github, homepage
3. ProteinMPNN paper, github
4. ESMFold paper, github, homepage

Workflow and package

1. nextflow paper, github, homepage
2. snakemake paper, github, documentation
3. bioconda paper, github

Assembler

1. hifiasm paper, github
2. Verkko paper, github

Read aligner

1. hisat1+2 paper, github, homepage
2. minimap2 paper, github
3. vsearch paper, github

Language models

1. ProtTrans paper, github
2. ESM paper, github
3. MSA Transformer paper, github

Variant caller

1. freebayes paper, github
2. pilon paper, github
3. Manta paper, github

Pangenomes

1. VG paper, github
2. Minigraph paper, github

Other topics

1. Conterminator paper, github
2. GTDB paper1, paper2, github