Softparsmap – Gene Tree Species Tree Reconicilation using Parsimony

Softparsmap

:: DESCRIPTION

Softparsmap is a java package that uses ’soft parsimony’ to root gene trees by mapping them on to a species tree.

::DEVELOPER

Liberles Research Group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 Softparsmap

:: MORE INFORMATION

Citation

J Mol Evol. 2006 Aug;63(2):240-50. Epub 2006 Jul 7.
Optimal gene trees from sequences and species trees using a soft interpretation of parsimony.
Berglund-Sonnhammer AC1, Steffansson P, Betts MJ, Liberles DA.

STEM 2.0 / STEM-hy 1.0 – Species Tree Estimation using Maximum likelihood (with hybridization)

STEM 2.0 / STEM-hy 1.0

:: DESCRIPTION

STEM-hy is a program for inferring maximum likelihood species trees from a collection of estimated gene trees under the coalescent model

::DEVELOPER

Laura S. Kubatko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 STEM / STEM-hy

:: MORE INFORMATION

Citation

Kubatko, L., B. C. Carstens, and L. L. Knowles. 2009.
STEM: Species Tree Estimation using Maximum likelihood for gene trees under coalescence,
Bioinformatics (2009) 25 (7): 971-973.doi: 10.1093/bioinformatics/btp079

GraphDTL v004 – Graph Reconciliation for Species Tree S and Gene Tree G

GraphDTL v004

:: DESCRIPTION

GraphDTL is the first method to infer supports for evolutionary events based on their frequencies in the set of equally parsimonious reconciliations
Given a , this program computes

::DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GraphDTL

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2013 Apr;11(2):1250025. doi: 10.1142/S0219720012500254. Epub 2012 Dec 28.
Representing a set of reconciliations in a compact way.
Scornavacca C1, Paprotny W, Berry V, Ranwez V.

STELLS2 – Inferring Species Tree from Gene Tree Topologies

STELLS2

:: DESCRIPTION

STELLS2 is a program for finding the maximum likelihood estimate of the species tree for the given gene trees, which undergo incomplete lineage sorting.

::DEVELOPER

Yufeng Wu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 STELLS

 :: MORE INFORMATION

Citation:

Wu Y.
A Coalescent-based Method for Population Tree Inference with Haplotypes.
Bioinformatics. 2014 Oct 24. pii: btu710.

Yufeng Wu
Coalescent-based Species Tree Inference from Gene Tree Topologies Under Incomplete Lineage Sorting by Maximum Likelihood
Evolution, v. 66 (3), p. 763-775, 2012

MixTreEM – Species Tree Inference Using a Mixture Model

MixTreEM

:: DESCRIPTION

MixTreEM (Mixture of Trees using Expectation Maximization) is a species tree reconstruction method.

::DEVELOPER

Ikram Ullah

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MixTreEM

:: MORE INFORMATION

Citation:

Species Tree Inference Using a Mixture Model.
Ullah I, Parviainen P, Lagergren J.
Mol Biol Evol. 2015 Sep;32(9):2469-82. doi: 10.1093/molbev/msv115.

simRRLs 1.5 – Simulate fastQ formatted RAD, ddRAD or GBS data on a fixed Species Tree

simRRLs 1.5

:: DESCRIPTION

The script simRRLs.py can be used to simulate RADseq-like sequences on a fixed species tree under a coalescent model. See Example usage page for advanced options, including simulating missing data, indels and different levels of divergence between taxa.

::DEVELOPER

Deren Eaton

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 simRRLs

:: MORE INFORMATION

ASTRAL 4.7.8 – Accurate Species TRee ALgorithm

ASTRAL 4.7.8

:: DESCRIPTION

ASTRAL is a Java program for estimating a species tree given a set of unrooted gene trees.

::DEVELOPER

Siavash Mirarab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Java JRE

:: DOWNLOAD

 ASTRAL

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jun 15;31(12):i44-i52. doi: 10.1093/bioinformatics/btv234.
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes.
Mirarab S, Warnow T

ASTRAL: genome-scale coalescent-based species tree estimation.
Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T.
Bioinformatics. 2014 Sep 1;30(17):i541-i548. doi: 10.1093/bioinformatics/btu462.

ConstraintChecker – Test Satisfiability/Consistency with Species Tree

ConstraintChecker

:: DESCRIPTION

ConstraintChecker is a python script that tests satisfiability/consistency with a species tree of a set of orthologies/paralogies/undecided.

::DEVELOPER

MANUEL LAFOND

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 ConstraintChecker

:: MORE INFORMATION

Citation

Manuel Lafond and Nadia El-Mabrouk
“Orthology and Paralogy Constraints: Satisfiability and Consistency”
RECOMB-CG 2014 paper (accepted)

gtp 0.15 – Gene Tree / Species Tree Reconciliation and Gene Tree Parsimony

gtp 0.15

:: DESCRIPTION

gtp is a software to infer gene duplication and speciation events on a gene tree.

::DEVELOPER

Mike Sanderson’s Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 gtp

:: MORE INFORMATION

Citation

A simple algorithm to infer gene duplication and speciation events on a gene tree.
Zmasek CM, Eddy SR.
Bioinformatics. 2001 Sep;17(9):821-8.

STAR-MP 1.0 – Species Tree informed Architecture Reconstruction – Maximum Parsimon

STAR-MP 1.0

:: DESCRIPTION

STAR-MP is a phylogenetic software for reconstructing domain architecture evolution through maximum parsimony given a known species tree, extant architectures, and (reconstructed) module (domain) phylogenies.

::DEVELOPER

Yi-Chieh Wu @ MIT Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • Numpy
  • Networkx

:: DOWNLOAD

 STAR-MP

:: MORE INFORMATION

Citation

Evolution at the Subgene Level: Domain Rearrangements in the Drosophila Phylogeny
Yi-Chieh Wu, Matthew D. Rasmussen, and Manolis Kellis.
Mol Biol Evol (2012) 29 (2):