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bio-pdb-structure-modification
Reference examples tested with: BioPython 1.83+, numpy 1.26+ Before using code patterns, verify installed versions match. If versions differ: Python: ...
bio-phasing-imputation-haplotype-phasing
wget https://faculty.washington.edu/browning/beagle/beagle.22Jul22.46e.jar java -jar beagle.22Jul22.46e.jar \ gt=input.vcf.gz \ out=phased java -jar b...
bio-phylo-modern-tree-inference
Build maximum likelihood phylogenetic trees with automatic model selection and ultrafast bootstrap. iqtree2 -s alignment.fasta -m MFP -B 1000 -T AUTO ...
bio-phylo-tree-io
Parse, write, and convert phylogenetic tree files in various formats. from Bio import Phylo from io import StringIO | Format | Extension | Description...
bio-pileup-generation
Generate pileup data for variant calling and position-level analysis. Pileup shows all reads covering each position in the reference, used for: Varian...
bio-population-genetics-association-testing
GWAS analysis using PLINK 2.0's unified --glm command for case-control and quantitative traits. plink2 --bfile data --glm --out results plink2 --bfile...
bio-population-genetics-linkage-disequilibrium
Calculate LD statistics, prune correlated variants, and identify haplotype blocks. plink2 --bfile data --r2 --ld-window-kb 1000 --ld-window-r2 0.2 --o...
bio-population-genetics-population-structure
Analyze genetic ancestry and population stratification using PCA and ADMIXTURE. plink2 --bfile data --pca 10 --out pcaresults plink2 --bfile data --pc...
bio-population-genetics-selection-statistics
Detect natural selection signatures using diversity statistics and extended haplotype homozygosity. import allel import numpy as np callset = allel.re...
bio-primer-design-primer-validation
Check primers for secondary structures, dimers, and other issues using primer3-py. import primer3 primer = 'ATGCGATCGATCGATCGATC' hairpin = primer3.ca...
bio-primer-design-qpcr-primers
Design primers and internal probes for quantitative PCR using primer3-py. import primer3 from Bio import SeqIO sequence = 'ATGCGTACGATCGATCGATCGATCGAT...
bio-proteomics-dia-analysis
Reference examples tested with: numpy 1.26+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: Python: pip ...