fastmulrfs's Introduction

FastMulRFS

FastMulRFS is a pipeline for estimating species trees from multi-copy gene trees, based on the Robinson-Foulds supertree problem for MUL-trees (MulRF). See this example.

PYTHON DEPENDENCIES

Python 3
DendroPy if using version 1
TreeSwift if using version 2 or version 3 (recommended)

OTHER DEPENDENCIES (see install instructions here)

CITATIONS

Citation for FastMulRFS:

@article{molloy2020fastmulrfs,
  author = {Molloy, Erin K. and Warnow, Tandy},
  title = {{FastMulRFS: Fast and accurate species tree estimation under generic gene duplication and loss models}},
  year = {2020},
  journal = {Bioinformatics},
  volume = {36},
  number = {Supplement_1},
  pages = {i57--i65},
  doi = {10.1093/bioinformatics/btaa444}
}

Citations for dependencies:

@article{moshiri2020treeswift,
  author = {N. Moshiri},
  title = {{TreeSwift: a massively scalable Python package for trees}},
  year = {2020},
  journal = {SoftwareX},
  volume = {11},
  pages = {100436},
  doi = {10.1016/j.softx.2020.100436}
}

@article{vachaspati2017fastrfs,
  author = {P. Vachaspati and T. Warnow},
  title = {{FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization}},
  year = {2017},
  journal = {Bioinformatics},
  volume = {33},
  number = {5},
  pages = {631--639},
  doi = {10.1093/bioinformatics/btw600}
}

@article{zhang2018astral3,
  author = {C. Zhang and M. Rabiee and E. Sayyari and S. Mirarab},
  title = {{ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees}},
  year = {2018},
  journal = {BMC Bioinformatics},
  volume = {19},
  number = {Suppl 6},
  pages = {153},
  doi = {10.1186/s12859-018-2129-y}
}