SPIMAP 1.1 – Species Informed Maximum A Posteriori Gene Tree Reconstruction

SPIMAP 1.1

:: DESCRIPTION

SPIMAP is a phylogenetic reconstruction method specifically designed for reconstructing gene trees in the case of a known species tree.

::DEVELOPER

Matt Rasmussen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler
  • Python

:: DOWNLOAD

 SPIMAP 

:: MORE INFORMATION

Citation

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction
Matthew D. Rasmussen and Manolis Kellis.
Mol Biol Evol (2011) 28 (1): 273-290.

MP-EST 2.0 – Estimating Species Trees from a set of Gene Trees

MP-EST 2.0

:: DESCRIPTION

MP-EST estimates species trees from a set of gene trees by maximizing a pseudo-likelihood function.

::DEVELOPER

Phylogenetics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/ Windows

:: DOWNLOAD

MP-EST

:: MORE INFORMATION

Citation

Liu, L., L. Yu, S.V. Edwards.
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model.
BMC Evol. Biol. 2010, 10:302.

DLCpar v1.1 – Reconciles Gene Trees to Species Trees through Maximum Parsimony

DLCpar v1.1

:: DESCRIPTION

DLCpar is a reconciliation method for inferring gene duplications, losses, and coalescence (accounting for incomplete lineage sorting).

::DEVELOPER

Yi-Chieh Wu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • NetworkX

:: DOWNLOAD

DLCpar

:: MORE INFORMATION

Citation

Genome Res, 24 (3), 475-86 Mar 2014
Most Parsimonious Reconciliation in the Presence of Gene Duplication, Loss, and Deep Coalescence Using Labeled Coalescent Trees
Yi-Chieh Wu , Matthew D Rasmussen, Mukul S Bansal, Manolis Kellis

TreeFix 1.1.10 / TreeFix-DTL 1.0.2 – Statistically Informed Gene Tree Error Correction using Species Trees

TreeFix 1.1.10 / TreeFix-DTL 1.0.2

:: DESCRIPTION

TreeFix is a phylogenetic method for improving gene tree reconstructions using a test statistic for likelihood equivalence and a species tree aware (reconciliation) cost function.

TreeFix-DTL is a phylogenetic program for reconstructing highly accurate prokaryotic gene trees.

::DEVELOPER

Yi-Chieh Wu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • C Compiler

:: DOWNLOAD

  TreeFix / TreeFix-DTL

:: MORE INFORMATION

Citation

TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees
Yi-Chieh Wu, Matthew D. Rasmussen, Mukul S. Bansal, and Manolis Kellis.
Systematic Biology. 2013. doi: 10.1093/sysbio/sys076

Improved Gene Tree Error-Correction in the Presence of Horizontal Gene Transfer.
Bansal MS, Wu YC, Alm EJ, Kellis M.
Bioinformatics. 2014 Dec 5. pii: btu806.

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.

COALGF Calculator 1.0 – Computing Probabilities of Gene Tree Histories Given Species Trees Under the Coalescent Process with Gene Flow

COALGF Calculator 1.0

:: DESCRIPTION

COALGF Calculator is a C program that will compute the probability distribution of gene tree histories and gene tree topolgies for a fixed three-taxon species tree under the coalescent model with gene flow between both pairs of sister population.

::DEVELOPER

Laura S. Kubatko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

COALGF Calculator

:: MORE INFORMATION

Citation

Distribution of coalescent histories under the coalescent model with gene flow.
Tian Y, Kubatko LS.
Mol Phylogenet Evol. 2016 Dec;105:177-192. doi: 10.1016/j.ympev.2016.08.024.

GeneRax 1.0.0 – Maximum Likelihood based Gene Tree Inference

GeneRax 1.0.0

:: DESCRIPTION

GeneRax is a tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss.

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

GeneRax

:: MORE INFORMATION

Citation

Benoit Morel, Alexey M. Kozlov, Alexandros Stamatakis, Gergely Szöllősi.
GeneRax: A tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss.
bioRxiv, 779066, 2019

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

TERA 1.1 – Tree Estimating using Reconciliation and Amalgamation

TERA 1.1

:: DESCRIPTION

Given a dated species tree S, a set of gene trees G, and a set of costs for gene events (duplications, transfers and losses), TERA computes the score of a most parsimonious reconciliation (MPR).

::DEVELOPER

Institut des Sciences de l’Evolution de Montpellier (ISEM)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 TERA

:: MORE INFORMATION

Citation

Joint Amalgamation of Most Parsimonious Reconciled Gene Trees.
Scornavacca C, Jacox E, Szöllősi GJ.
Bioinformatics. 2014 Nov 6. pii: btu728.