B cell phylogenetic inference package — igphyml 1.0.7 documentation (original) (raw)
**IMPORTANT!**IgPhyML has moved to https://github.com/immcantation/igphyml
To update Git configuration settings use:
git config user.email “your-gh-user@email.com” git config user.name “your-gh-user-name” git remote set-url origin git@github.com:immcantation/igphyml.git
IgPhyML is a program designed to build phylogenetic trees and test evolutionary hypotheses regarding B cell affinity maturation.
The biology of B cell somatic hypermutation (SHM) violates important assumptions in most standard phylogenetic substitution models; further, while most phylogenetics programs are designed to analyze single lineages, B cell repertoires typically contain thousands of lineages. IgPhyML addresses both of these issues by implementing substitution models that correct for the context-sensitive nature of SHM, and combines information from multiple lineages to give more precisely estimated repertoire-wide model parameter estimates.
IgPhyML is integrated into the Immcantation framework, meaning users can easily build and visualize B cell lineage trees and test hypotheses about mutation and selection in B cell repertoires.
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