Reproducible Quantitative Methods for EEB
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Updated
Jan 27, 2021 - TeX
Reproducible Quantitative Methods for EEB
PyPop: Python for Population Genomics
a versatile toolkit for processing and analyzing diverse types of sequence data
Create, modify and analyse phylogenetic trees in R
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
Evolutionary simulation where agents age, reproduce, and eat each other
R package: BALCONY (Better ALignment CONsensus analYsis)
HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃♀️
Newick formatted (phylogenetic) trees
Bio-ModelChecker: Using Bounded Constraint Satisfaction to Seamlessly Integrate Observed Behavior with Prior Knowledge of Biological Networks
Shiny app visualizing the effects of carbonate stratigraphy on trait evolution
A simple python3 program to compare aligned DNA/protein sequences.
a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
R codes for simulating and detecting punctuated evolution in any clades, from dinosaurs to viruses
a broadly applicable tool for automated gene identification and retrieval
A collection of work investigating the potentiation of associative learning in digital organisms
Site for the April 2022 Software Carpentry workshop, run through the UCLA EEB department by Kaija Gahm, Maddi Cowen, and Kenji Hayashi
HARE: Genetic Feature Enrichment Analysis Pipeline
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