Archive
Nucleotide Sequence Visualization
👁️ Python library to plot DNA sequence features (e.g. from Genbank files) https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer
Nucleotide Sequence Optimization
NUPACK - analysis and design of nucleic acid structures, devices, and systems. http://nupack.org/ DNA Chisel - a versatile sequence optimizer paper on …
LSTrAP
installation dependency Required Tools Bowtie2 TopHat HISAT2 Samtools SRAtools HTSeq + all dependencies (including PySam) Python 3.5 + SciPy + Numpy …
bio_embedding
installation pip install bio_embeddings[all] usage bio_embeddings /scratch/ch29576/common-scripts/bio_embedding/parameters_blueprint.yml worth mention …
DISOPRED 3 -
download ftp: http://bioinfadmin.cs.ucl.ac.uk/downloads/DISOPRED/ althought the archive marked as version three, the folder name in inside is still 2? …
Broccoli - infer with high precision orthologous groups and pairs of proteins using a mixed phylogeny-network approach
https://github.com/rderelle/Broccoli dependency DIAMOND Fasttree manual https://github.com/rderelle/Broccoli/blob/master/manual_Broccoli_v1.2.pdf …
NLR-annotator
https://github.com/steuernb/NLR-Annotator Requirements MEME suite and JRE are already on GACRC sapelo2, just module load them. Usage and scripts …
phylogenetic analysis
phylogenetic network implicit vs. explicit genes trees do not match estimation error incomplete lineage sorting gene flow
OrthoFinder
comparative genomics
jupyter lab
things I wish that I know when I started to use jupyter lab
jetson nano 2Gb
AIOT toy
HMMER
using HMMER with Pfam
Meme
how the internet works#bioinformatics #meme #fun #geek #coding #datascience #IT #software #engineering #fyp #synthwave #biopython #python #biology …