Paper

Address correspondence to: Yi-Chieh Wu (yjw AT cs DOT hmc DOT edu)

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PLCT is a package for understanding gene tree evolution through gene duplications, losses, and coalescence with multiple samples per species.

• Latest version (v1.0, 07/20/2016)
• Change Log

• Python (2.7.1 or greater): http://python.org
• NetworkX (1.7 or greater): http://networkx.github.io

Supplemental data

In our paper, we evaluated feasibility using 6798 real gene families across 7 ape genomes, as well as simulated gene families across the 12 Drosophila clade.

• Species trees: apes.stree, flies.stree
  Species maps: apes.smap, flies.smap
  Species abbreviations: flies.names.txt
  

  PLCT does not require a species tree. However, we provide the species trees, the species maps that specify which genes belong to which species, and the species name abbreviations for reference.

• Real ape dataset
  Alignments: real-apes.tar.gz (53M)
  Trees: PHYLIP (2.4M), BioNJ (2.5M), PhyML (2.8M), RAxML (3.2M)
  Feasibility analysis: real-apes-plct.tar.gz (127K)
  

  Filenames have the format FAMID.HAPLOTYPE.EXT. Alignments are in FASTA format and trees in Newick format.
  • FAMID: the gene family ID from Ensembl
  • HAPLOTYPE: the haplotype number (1,2)
  • EXT: align for alignments, tree for gene trees

• Simulated fly dataset
  Data: sim-flies.tar.gz (532M)
  Feasibility analysis: sim-flies-plct.tar.gz (128K)
  

  Each gene family is stored in its own directory sim-flies/POP-RATE/FAMID.
  • POP: the effective population size (1e6-100e6)
  • RATE: the (duplication and loss) rate multiplier (1x,2x,4x), where 1x is the rate observed in real data
  • FAMID: the gene family ID (0-499)
  Each directory has the following files:
  • the true reconciliation in DLCoal format:
    • FAMID.coal.tree: the gene tree in Newick format with named internal nodes
    • FAMID.coal.recon: the reconciliation mapping between the gene tree (*.coal.tree) and the locus tree (*.locus.tree)
    • FAMID.locus.tree: the locus tree in Newick format
    • FAMID.locus.recon: the reconciliation mapping between the locus tree (*.locus.tree) and the species tree (.stree)
    • FAMID.daughters: the set of daughter nodes
  • FAMID.coal.align: the simulated alignment in FASTA format
  • FAMID.coal.raxml.tree: the reconstructed gene tree in Newick format
  • the reconciliations, alignments, and trees for multiple samples per species (N=2,5,10): FAMID.coalN.tree, FAMID.coalN.recon, FAMID.coalN.align, FAMID.coalN.raxml.tree

Last updated 07/20/16.