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Modeling gene duplication, loss, and coalescence (through parsimony)
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DLCpar http://compbio.mit.edu/dlcpar/ Yi-Chieh Wu, with libraries contributed from Matthew Rasmussen ============================================================================= ABOUT DLCpar is a reconciliation program that maps a gene tree to a species tree by inferring gene duplications, losses, and coalescence (accounting for incomplete lineage sorting). DLCpar uses the labeled coalescent tree (LCT) to infer the species and locus to which a gene belongs. DLCpar citation: Wu, Rasmussen, Bansal, Kellis. Most Parsimonious Reconciliation in the Presence of Gene Duplication, Loss, and Deep Coalescence using Labeled Coalescent Trees. Genome Research (24)3:475-486, 2014. This package includes the Python source code of the DLCpar program, as well as several useful utilities for working with LCTs. ============================================================================= USAGE Running dlcpar with no arguments will print out its command-line usage. #============================================================================= # File formats Labeled Coalescent Tree (LCT) -- used by DLCpar X.tree -- coalescent tree (newick) X.recon -- reconciliation from coal tree to species tree and locus set col1 = coal node ID col2 = species node ID col3 = locus X.order -- partial order of coal tree nodes col1 = species node ID col2 = parent locus col3 = (ordered) list of coal node IDs (comma-separated) Three Tree Model (3T) -- used by DLCoalRecon X.coal.tree -- coalescent tree (newick) X.coal.recon -- reconciliation from coal tree to locus tree col1 = coal node ID col2 = locus node ID col3 = event ("none") X.locus.tree -- locus tree (newick) X.locus.recon -- reconciliation from locus tree to species tree col1 = locus node ID col2 = species node ID col3 = event ("gene", "spec", "dup") X.daughters -- daughter nodes in locus tree (one per line) #============================================================================= # Examples See examples/test.sh for an example of how to use each program in this package.
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