:: DESCRIPTION
MP-EST estimates species trees from a set of gene trees by maximizing a pseudo-likelihood function.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
DLCpar is a reconciliation method for inferring gene duplications, losses, and coalescence (accounting for incomplete lineage sorting).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
Softparsmap is a java package that uses ’soft parsimony’ to root gene trees by mapping them on to a species tree.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
GeneRax is a tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: DESCRIPTION
COAL is a program for computing gene tree probabilities and simulating gene trees in species trees under the coalescent model.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Degnan, JH and LA Salter. 2005.
Gene tree distribtutions under the coalescent process.
Evolution 59(1): 24-37.
:: DESCRIPTION
MRC.py is a computer program to evaluate the compatibility lengths given supertrees and gene trees and to extract the supertrees with the minimal lengths
::DEVELOPER
the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
