DLCpar
http://compbio.mit.edu/dlcpar/
Yi-Chieh Wu, with libraries contributed from Matthew Rasmussen

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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.
In prep.

This package includes the Python source code of the DLCpar program,
as well as several useful utilities for working with LCTs.


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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.
