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The ipcoal ethos
Terminology and units
Installation
Tutorial
Empirical Example
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Welcome to ipcoal’s documentation!
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Welcome to ipcoal’s documentation!
¶
The ipcoal ethos
Our goals
Contact us
Terminology and units
Terminology
Units
Installation
Conda installation
Developers welcomed
Dependencies
Tutorial
Getting started
The species tree
The demographic model
Simulating genealogies
The results dataframe (.df)
Drawing trees
Demographic parameters (Ne)
Demographic parameters (admixture)
Simulating sequences
Inferring gene trees from sequences
Analysis tools
Empirical Example
Mammal phylogeny data set
Filtering and selecting taxa
Plot tree with Ne and g values
Convert edge lengths from time to generations
Examine the distribution of genealogy lengths
Simulate unlinked loci (e.g., UCE)
Examine expected variation in inferred gene trees
Simulate on a larger clade
FAQs
Mutation rate variation across the tree
Generation time variation across the tree
Converting to generations from a time-scaled tree
Converting to generations from a coalescent-unit scaled tree
How can I simulate a large locus or chromosome?
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