Who is Who in Phylogenetic Networks

Programs and their Input Data

Below, you can find all programs present at least 1 time(s) in Who is who in phylogenetic networks, as well as the links with the data they use as input.

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Program List

115 programs to compute, evaluate, compare, visualize... phylogenetic networks. This page is automatically built from all publications tagged by Program* in the database.

Program AdmixTools

Available at http://genetics.med.harvard.edu/reich/Reich_Lab/Software_files/admixtools_v2.tar 1 publication in the database mentions Program AdmixTools

Program ALE

ALE is a C++ program which, given one or more gene trees and an ultrametric species tree, returns a reconciled gene tree annotated with duplication transfer and loss events, its likelihood, as well as optimal rates of duplication, transfer and loss. Available at https://github.com/ssolo/ALE. 2 publications in the database mention Program ALE

Program Angst

Available at http://almlab.mit.edu/angst/ 2 publications in the database mention Program Angst

Program Arlequin

The goal of Arlequin is to provide the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples. In particular, Arlequin implements a Minimum Spanning Network algorithm to embed the set of all minimum spanning trees computed from a distance matrix of haplotypes (http://cmpg.unibe.ch/software/arlequin3/). 5 publications in the database mention Program Arlequin

Program ARTNET

1 publication in the database mentions Program ARTNET

Program Beagle

Beagle is a small collection of related programs for analysing the minimum number of recombinations required for a SNP data set under the infinite sites model. Available at http://www.stats.ox.ac.uk/~lyngsoe/beagle/. 3 publications in the database mention Program Beagle

Program BIMLR

BIMLR is a Java program which takes as input a set of rooted phylogenetic trees in the Newick format and outputs a rooted phylogenetic networks in the extended Newick format. The approach is based on softwired clusters. Software available at http://nclab.hit.edu.cn/~wangjuan/BIMLR/ 3 publications in the database mention Program BIMLR

Program Bio PhyloNetwork

Bio-PhyloNetwork is a Perl package that relies on the BioPerl bundle and implements many algorithms on phylogenetic networks (http://dmi.uib.es/~gcardona/BioInfo/Bio-PhyloNetwork.tgz). It is used in a Java Applet which can compare and draw two phylogenetic networks entered in eNewick format with the same set of leaves (http://dmi.uib.es/~gcardona/BioInfo/alignment.php) 4 publications in the database mention Program Bio PhyloNetwork

Program BMhyd

BMhyd is an R package to analyze the phenotypic evolution of species of hybrid origin on a phylogenetic network. Available at https://cran.r-project.org/web/packages/BMhyd/ 1 publication in the database mentions Program BMhyd

Program Clustistic

CLUSTISTIC is a Java program which, given a set T of rooted binary trees on the same set of taxa, constructs (all) networks with a minimum number of reticulations that represent the set of clusters induced by the trees in T (in the softwired sense). Available at http://skelk.sdf-eu.org/clustistic/ 2 publications in the database mention Program Clustistic

Program CMPT

CMPT is an ANSI-C software which takes as input a set of rooted trees on the same taxa set (Newick format) and outputs a rooted explicit non necessarily binary phylogenetic network containing them with the minimum number of reticulation vertices (extended Newick format). Available at http://www.cs.cityu.edu.hk/~lwang/software/mtree/cmpt.html 2 publications in the database mention Program CMPT

Program CombineTrees

CombineTrees combines MP trees into a single (possibly reticulated) graph. Available at http://applications.lanevol.org/combineTrees. 2 publications in the database mention Program CombineTrees

Program ConsensusNetwork

Available at http://www.info2.uqam.ca/~makarenkov_v/ConsensusNetwork.rar 1 publication in the database mentions Program ConsensusNetwork

Program constNJ

constNJ is an OCaml program which takes as input a set of distances matrices and implicitly reconstructs a phylogenetic network: it infers, for each of those matrices, a corresponding phylogenetic tree, with some constraints on the upper bound of the SPR-distance between those reconstructed trees. Available at http://www.stat.berkeley.edu/~matsen/constNJ/. 1 publication in the database mentions Program constNJ

Program CycleKiller

CycleKiller is a Java program which takes as input two rooted binary trees and builds a phylogenetic network containing both of them, minimizing the number of reticulations with a 2-approximation algorithm. Available at http://skelk.sdf-eu.org/cyclekiller/ 3 publications in the database mention Program CycleKiller

Program Dendroscope

Dendroscope is a Java software for visualizing phylogenetic trees and rooted networks. It is interactive, and also provides methods to reconstruct or compare phylogenetic networks. Available at www.dendroscope.org. 17 publications in the database mention Program Dendroscope

Program ecceTERA

Given a dated species tree S, a set of gene trees G, and a set of costs for gene events duplications, transfers and losses, ecceTERA computes the score of a most parsimonious reconciliation (MPR). Source code available at http://mbb.univ-montp2.fr/MBB/uploads/ecceTERA_1_2_4.tar.gz. Software available online at http://mbb.univ-montp2.fr/MBB/subsection/softExec.php?soft=eccetera. 1 publication in the database mentions Program ecceTERA

Program EEEP

EEEP is a program that reconciles a rooted reference tree and an unrooted "test" tree by performing the smallest number of subtree prune-and-regraft (SPR) operations on the reference tree. The effect of these SPR operations in analogous to that of lateral genetic transfer events, so the reconciliation path output by the program is equivalent to a set of lateral gene transfers between organisms in the reference tree. http://bioinformatics.org.au/eeep/ . 3 publications in the database mention Program EEEP

Program FastHN

FastHN is an ANSI C program which takes two rooted binary trees as input and constructs a rooted explicit phylogenetic network containing them. It is available at http://rnc.r.dendai.ac.jp/~chen/fastHN.html 1 publication in the database mentions Program FastHN

Program FastNet

Available at https://gitlab.msu.edu/liulab/FastNet.data.scripts. 2 publications in the database mention Program FastNet

Program FlatNJ

4 publications in the database mention Program FlatNJ

Program Frin

Available at https://github.com/wangjuanimu/Frin 1 publication in the database mentions Program Frin

Program Fylogenetica

Fylogenetica is a Java program which takes as input a dense quartet set and builds and displays an unrooted level-1 phylogenetic network containing them, if it exists. Available at http://sourceforge.net/projects/fylogenetica/. 1 publication in the database mentions Program Fylogenetica

Program GalledTree

GalledTree can determine if the input sequences can be reconstructed with a galled-tree network (http://wwwcsif.cs.ucdavis.edu/~gusfield/galledtree.tar) 1 publication in the database mentions Program GalledTree

Program GraphDTL

Given a dated species tree and a gene tree, GraphDTL computes a graph reconciliation for these two trees. Available at http://celinescornavacca.wordpress.com/software/ 2 publications in the database mention Program GraphDTL

Program HapBound

HapBound computes lower bounds on the number of recombinations needed to generate a set of binary sequences under the infinite sites assumption (http://www.cs.ucdavis.edu/~yssong/lu.html). 1 publication in the database mentions Program HapBound

Program HGT_simul

Available at http://mbb.univ-montp2.fr/MBB/download_sources/13__HGT_simul. 1 publication in the database mentions Program HGT_simul

Program HiDe

1 publication in the database mentions Program HiDe

Program HorizStory

HorizStory is a program that approximates the SPR distance between two rooted and possibly multifurcating trees to reconciliate them inside a network. It is available from Eric Bapteste upon request and was http://coffee.biochem.dal.ca/ 2 publications in the database mention Program HorizStory

Program Hybrid-coal

1 publication in the database mentions Program Hybrid-coal

Program Hybrid-Lambda

Hybrid-Lambda takes as input a rooted species network in the extended Newick format and simulates a gene tree within the network under the coalescent process. Available at https://github.com/shajoezhu/hybrid-Lambda 3 publications in the database mention Program Hybrid-Lambda

Program HybridInterleave

HybridInterleave is a Java program for an exact calculation of the minimum number of hybridization events to explain two rooted binary phylogenetic trees on the same taxa set. Available at http://www.math.canterbury.ac.nz/~c.semple/software.shtml. 5 publications in the database mention Program HybridInterleave

Program HybridNET

HybridNET is a Linux or Windows program to compute the hybrid number of two rooted phylogenetic trees. It is experimentally a faster implementation than HybridInterleave. It is available at http://www.cs.cityu.edu.hk/~lwang/software/Hn/treeComp.html 2 publications in the database mention Program HybridNET

Program HybridNumber

HybridNumber is a Perl script for an exact calculation of the minimum number of hybridization events to explain two rooted binary phylogenetic trees on the same taxa set (download here). It was replaced by the more efficient HybridInterleave. 3 publications in the database mention Program HybridNumber

Program Hybroscale

Available at a href https: drupal.bio.ifi.lmu.de en softwareservices hybroscale index.html https: drupal.bio.ifi.lmu.de en softwareservices hybroscale index.html a 6 publications in the database mention Program Hybroscale

Program icelu-PhyloNetwork

icelu-PhyloNetwork is a C program which, given a rooted phylogenetic network and a set of taxa, decides if the set of taxa is a softwired cluster of the network; given two rooted phylogenetic networks, computes the softwired cluster distance between them. Available at https://github.com/icelu/PhyloNetwork. 1 publication in the database mentions Program icelu-PhyloNetwork

Program IcyTree

1 publication in the database mentions Program IcyTree

Program IGNet

1 publication in the database mentions Program IGNet

Program ILPEACE

ILPEACE is a Java program which builds a duplication-loss-transfer scenario to reconcile a rooted binary gene tree and species tree, using the ILP solver CPLEX. Available at http://homepages.cwi.nl/~iersel/ilpeace. 1 publication in the database mentions Program ILPEACE

Program JML

JML is a program that implements a posterior predictive checking method to detect hybridization events. Available at http://www.plantevolution.org/jml.html 1 publication in the database mentions Program JML

Program JPrIME-DLTRS

JPrIME-DLTRS, also called DELETERIOUS, is a Java application inferring an unknown gene tree in light of a known and dated species tree and known sequence data for the leaves, using the DLTRS model (duplication, loss, lateral transfer (LGT) events, and sequence evolution with a relaxed molecular clock). Available at https://code.google.com/p/jprime/wiki/DLTRS. 1 publication in the database mentions Program JPrIME-DLTRS

Program LatTrans

LatTrans is a program which identifies lateral gene transfer events from two rooted phylogenetic trees. It was available at www.cs.mcgill.ca/~laddar/lattrans. 5 publications in the database mention Program LatTrans

Program LEV1ATHAN

LEV1ATHAN is a Java program for generating level-1 networks from sets of rooted triplets. It implements a heuristic to find a level-1 network consistent with as many of the input triplets as possible. Available at http://skelk.sdf-eu.org/lev1athan/. 2 publications in the database mention Program LEV1ATHAN

Program Lev1Generator

Lev1Generator is a Java program which generates level-1 networks at the DOT format. It can be downloaded at http://www.uea.ac.uk/~x3002128/lev1generator/. 1 publication in the database mentions Program Lev1Generator

Program Level2

LEVEL2 is an implementation in Java of the algorithm of Leo van Iersel, Judith Keijsper, Steven Kelk and Leen Stougie which constructs level-2 phylogenetic networks from rooted triplets. http://skelk.sdf-eu.org/level2triplets.html 2 publications in the database mention Program Level2

Program LGTnetwork

LGTnetwork is a Python program which reconstructs a tree-based phylogenetic network from a principal rooted phylogenetic tree and secondary rooted phylogenetic trees. Available at http://bioinfo.uib.es/~recerca/LGTnetworks/ 1 publication in the database mentions Program LGTnetwork

Program lingpy

1 publication in the database mentions Program lingpy

Program LNetwork

LNetwork is a Java program which takes as input a set of rooted phylogenetic trees in the Newick format and outputs a rooted phylogenetic networks in the extended Newick format. Available at http://nclab.hit.edu.cn/~wangjuan/LNETWORK/ 4 publications in the database mention Program LNetwork

Program MaafB

2 publications in the database mention Program MaafB

Program Marlon

MARLON (Minimum Amount of Reticulation Level One Network) is a program which reconstructs a level-1 phylogenetic network (i.e. galled tree), with the minimum number of reticulation nodes, from a set of triplets. Available at http://skelk.sdf-eu.org/marlon.html. 3 publications in the database mention Program Marlon

Program MC-Net

MC-Net is a Matlab program to compute, from a distance matrix, a circular split system which can be visualized with SplitsTree. Available at http://bioinf.cs.ipm.ac.ir/softwares/mc.net/. 1 publication in the database mentions Program MC-Net

Program McKiTscH

McKiTscH implements a fixed-parameter algorithm for finding the minimum sequence of SPR moves between two trees. Available at http://www.mcb.mcgill.ca/~hallett/McKiTscH 1 publication in the database mentions Program McKiTscH

Program Mowgli

Mowgli is a C++ gene tree/species tree reconciliation program including time consistent transfers, duplications and losses. It gives the set of all optimal reconciliation scenarios given a dated species tree, a gene tree, as well as duplication, loss and horizontal transfer costs. Available at http://www.atgc-montpellier.fr/Mowgli/. 5 publications in the database mention Program Mowgli

Program MowgliNNI

Available at http://www.atgc-montpellier.fr/Mowgli/ 2 publications in the database mention Program MowgliNNI

Program MPNet

MPNet is a Java program (using CPLEX or GLPK) which takes as input a phylogenetic network (e-newick format) and a set of aligned sequences associated to its leaves (fasta format), and computes the softwired and hardwired parsimony score of a phylogenetic network. The results can be displayed with GraphViz where each edge is labeled by the number of character changes. Available at http://homepages.cwi.nl/~iersel/MPNet/ 1 publication in the database mentions Program MPNet

Program MY CLOSURE

MY-CLOSURE is a Java application for computing supernetworks from partial phylogenetic trees, which outputs a set of trees whose corresponding phylogenetic network can be visualized in SplitsTree. Available at http://www.uea.ac.uk/cmp/research/cmpbio/MyClosure. 1 publication in the database mentions Program MY CLOSURE

Program Nepal

Nepal is aimed mainly at providing a suite of tools for reconstructing and analyzing reticulate evolutionary relationships using the maximum parsimony (MP) and maximum likelihood (ML) criteria. http://bioinfo.cs.rice.edu/nepal/index.html 7 publications in the database mention Program Nepal

Program NetGen

NETGEN is an event-driven simulator for generating phylogenetic networks with DNA sequences, where the traditional birth-death model often used in biology to create phylogenetic trees is extended to support diploid hybrids and/or variable rate lineages. http://www.cs.unm.edu/~morin/sw.html 3 publications in the database mention Program NetGen

Program NetTest

NetTest is a web interface to display an explicit phylogenetic network and test whether it belongs to some restricted subclasses of networks: galled tree, tree-child, tree-sibling or time-consistent. It is available at http://darwin.uvigo.es/software/nettest/. 1 publication in the database mentions Program NetTest

Program NetView

NetView first reconstructs an NJ-phylogenetic tree from binary characters. Then the user can choose sites which are incompatible with the tree, then the tree is mapped to a network on two parallel planes in 3D which helps visualizing the conflicts. NetView was available at http://esper.lab.nig.ac.jp/netview/ 1 publication in the database mentions Program NetView

Program Network

Network is a free software that generates evolutionary trees and networks from genetic, linguistic, and other data. It can then provide age estimates for any ancestor in the tree. http://www.fluxus-engineering.com/sharenet.htm 5 publications in the database mention Program Network

Program Notung

2 publications in the database mention Program Notung

Program PADRE

PADRE is a Java software package allowing the computation and graphical representation of reticulate networks from Multi-Labelled (MuL) Trees. The network is constructed in stages which allows the user flexibility in choosing appropriate elements of the input tree for merging. http://www.uea.ac.uk/cmp/research/cmpbio/PADRE. 7 publications in the database mention Program PADRE

Program Phangorn

Phangorn is an R package which provides methods to reconstruct phylogenetic trees, and a method to reconstruct a split network. Available at http://cran.r-project.org/web/packages/phangorn/index.html. 2 publications in the database mention Program Phangorn

Program PhippsNetwork

PhippsNetwork is a Java software which takes as input a circular split system built by SplitsTree from distances, and which outputs a planar split network with few faces approximating the distances. Available at http://www.utdallas.edu/~sxb027100/PhippsNetwork/. 2 publications in the database mention Program PhippsNetwork

Program PhyloDAG

Available at https://phylomemetic.wordpress.com/2015/04/17/phylodag/. 2 publications in the database mention Program PhyloDAG

Program PhyloNet

PhyloNet is aimed mainly at providing a suite of tools for reconstructing and analyzing reticulate (non-treelike) evolutionary relationships. In particular, the software package includes features for inferring horizontal gene transfer from a pair of species/gene trees, and detecting interspecific recombination breakpoints in a sequence alignment. Further, it has the capabilities for reading/storing phylogenetic networks, and comparing phylogenetic networks topologies. http://bioinfo.cs.rice.edu/phylonet/index.html 22 publications in the database mention Program PhyloNet

Program PhyloNet-HMM

Available at http://bioinfo.cs.rice.edu/software/phmm 1 publication in the database mentions Program PhyloNet-HMM

Program PhyloNetwork

PhyloNetwork is a Python package to deal with phylogenetic networks (create a network from its eNewick representation, computing distances between networks, etc.). Available at https://pypi.python.org/pypi/phylonetwork/1.0b6 (on GitHub: original, forked version) 4 publications in the database mention Program PhyloNetwork

Program PhyloNetworks SNaQ

PhyloNetworks (including SNaQ) is a Julia package for statistical inference, data manipulation and visualization of phylogenetic networks. More precisely, it implements the SNaQ method which reconstructs a level 1 network from a set of unrooted gene trees, possibly with some uncertainty values. It uses GraphViz to display the output network. Available at https://github.com/crsl4/PhyloNetworks 9 publications in the database mention Program PhyloNetworks SNaQ

Program PhyloSketch

1 publication in the database mentions Program PhyloSketch

Program PIRN

PIRN (for "Parsimonious Inference of Reticulate Network") is a C++ program which reconstructs a minimum reticulate network from a set of rooted trees. It can be downloaded at http://www.engr.uconn.edu/~ywu/PIRN.html. 9 publications in the database mention Program PIRN

Program PopART

Available at http://popart.otago.ac.nz/index.shtml 1 publication in the database mentions Program PopART

Program Prunier

Prunier is a C++ program which detects lateral gene transfers by statistical reconciliation of phylogenetic forests: given a rooted or unrooted species tree, gene sequences, and an optional gene tree (otherwise one is reconstructed from the sequence data), it tries to reconcile both trees and outputs a scenario of lateral gene transfers. Available at http://pbil.univ-lyon1.fr/software/prunier/ 2 publications in the database mention Program Prunier

Program Pyramids

Pyramids computes a pyramidal classification from a dissimilarity matrix. It was available at http://genome.genetique.uvsq.fr/Pyramids. 3 publications in the database mention Program Pyramids

Program QNet

QNet is a software package written in Java which encompasses methods for generating phylogenetic networks from quartet data (http://www2.cmp.uea.ac.uk/~vlm/qnet/). 6 publications in the database mention Program QNet

Program Quartet

Quartet-Imputation Supernetworks implements a supernetwork method and reconstructs a split network from a set of unrooted trees, possibly on different taxa sets. The program is available at http://awcmee.massey.ac.nz/downloads_software.htm and its documentation at http://awcmee.massey.ac.nz/software_downloads/quartet/Quartet_help.htm 1 publication in the database mentions Program Quartet

Program Quartet Decomposition

1 publication in the database mentions Program Quartet Decomposition

Program QuartetMethods

QuartetMethods is a C++ program which reconstructs a split network from a set of weighted quartets. Available at http://sysbio.cvm.msstate.edu/QuartetMethods/ 1 publication in the database mentions Program QuartetMethods

Program QuartetNet

2 publications in the database mention Program QuartetNet

Program QuasiDec

QuasiDec is a C++ extension of the software system polymake which computes the block decomposition of a quasi-median graph corresponding to a set of aligned input sequences (http://www.uea.ac.uk/cmp/research/cmpbio/quasidec). 1 publication in the database mentions Program QuasiDec

Program QuickCass

1 publication in the database mentions Program QuickCass

Program RANGER-DTL

RANGER-DTL is a multiplatform program which takes as input a gene tree (rooted or unrooted) and a rooted species tree (dated or undated) and builds a duplication-transfer-loss scenario. Available at http://compbio.mit.edu/ranger-dtl/ 4 publications in the database mention Program RANGER-DTL

Program RecMin

Given an input set of sequence data, RecMin outputs two minimum numbers of recombination events; firstly, the statistic Rm of Hudson and Kaplan (1985), that employs the four-gamete test; and secondly, a new bound, Rh or Rs (described in Myers and Griffiths, 2003). http://www.stats.ox.ac.uk/~myers/ 1 publication in the database mentions Program RecMin

Program Recodon

Recodon is a population genetic simulator that generates samples of nucleotide and codon sequences from populations with recombination, migration and growth, after generating their genealogy (a phylogenetic network) under the coalescent framework. Available at http://darwin.uvigo.es/software/recodon.html. 3 publications in the database mention Program Recodon

Program RecPars

RecPars performs a parsimony analysis of a set of DNA sequences. It tries to find the best phylogenies for different segments of the sequences and thereby postulating a recombination event between these segments. Available at http://www.daimi.au.dk/~compbio/recpars/recpars.html. 1 publication in the database mentions Program RecPars

Program Reticlad

Reticlad is a program which tests reticulation events on terminal branches of a phylogenetic tree, where inputs are binary characters. It is available upon request from James D. Morefield. 2 publications in the database mention Program Reticlad

Program SAGE

Sage is a mathematical software which includes graph algorithms, including one adressed to phylogenetic networks: isomorphism test for binary rooted ones (function IsomorphismPhilo) 2 publications in the database mention Program SAGE

Program SAQ-Net

SAQ-Net is a Matlab program to compute, from a set of weighted quartets, a circular split system which can be visualized with SplitsTree. Available at http://bioinf.cs.ipm.ac.ir/softwares/saq.net/. 1 publication in the database mentions Program SAQ-Net

Program Serial NetEvolve

Serial NetEvolve is a modification of the Treevolve program in which serially sampled sequences are evolved along a randomly generated coalescent tree or network http://biorg.cis.fiu.edu/SNE/ 1 publication in the database mentions Program Serial NetEvolve

Program SHRUB

SHRUB constructs a minimum recombination phylogenetic network (ARG) that derives a set of binary sequences under the infinite sites assumption. SHRUB, SHRUB-GC 3 publications in the database mention Program SHRUB

Program Simplistic

SIMPLISTIC (SIMPLe network heurISTIC) is a program which reconstructs a level-k phylogenetic network consistent with a dense input triplet set, minimizing the level and the number of reticulations when possible. Available at http://skelk.sdf-eu.org/simplistic.html. 5 publications in the database mention Program Simplistic

Program Sliding MinPD

Sliding MinPD reconstructs evolutionary networks of serially-sampled sequences by combining minimum pairwise distance measures with automated recombination detection based on a sliding window approach (http://biorg.cis.fiu.edu/SlidingMinPD/). The resulting network can be build with the online network drawer at http://72.17.173.2:800/minpd/ 1 publication in the database mentions Program Sliding MinPD

Program SNSA

SNSA (Super Network-Simulated Annealing) is a Matlab program which takes a set of unrooted trees as input (Newick format) and outputs a supernetwork of those trees. Actually, it creates a split system which can be visualized as a split network in SplitsTree. Available at http://bioinf.cs.ipm.ir/software/snsa/. 2 publications in the database mention Program SNSA

Program Spectronet

Spectronet is a package for the analysis and visualization of complex evolutionary data that is not best represented by a bifurcating tree. Given an alignment in NEXUS format, the package works by computing a collection of weighted splits or bipartitions of the taxa and then allowing the user to interactively analyze the resulting collection using tools such as Lento-plots and median networks. http://awcmee.massey.ac.nz/spectronet/ 4 publications in the database mention Program Spectronet

Program SplitsTree

SplitsTree4 is the leading application for computing evolutionary networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks. Available at www.splitstree.org. 41 publications in the database mention Program SplitsTree

Program SPNet

SPNet can reconstruct a galled phylogenetic network containing two input trees allowing an arbitrary number of reticulations (program not available on the Internet). 5 publications in the database mention Program SPNet

Program SPRDist

SPRDist computes the SPR distance between two rooted trees, and will, in a next version, compute the hybridization number of two rooted trees with an Integer Linear Programming method. It can be downloaded at http://www.engr.uconn.edu/~ywu/SPRDist.html 1 publication in the database mentions Program SPRDist

Program SuperQ

SuperQ is a Java program which takes as input a set of partial unrooted trees with weighted edges and outputs a weighted circular split system which can be visualized in SplitsTree. Available at http://www.uea.ac.uk/cmp/research/cmpbio/superq. 1 publication in the database mentions Program SuperQ

Program SylvX

1 publication in the database mentions Program SylvX

Program T REX

T-REX (tree and reticulogram reconstruction) is an application to reconstruct phylogenetic trees and reticulation networks from distance matrices. http://www.labunix.uqam.ca/~makarenv/trex.html, internet version here. 14 publications in the database mention Program T REX

Program TCGenerators

1 publication in the database mentions Program TCGenerators

Program TCS

TCS is a Java computer program to estimate gene genealogies including multifurcations and/or reticulations (i.e. networks), using parsimony. http://darwin.uvigo.es/software/tcs.html. 9 publications in the database mention Program TCS

Program TERA

TERA is a C++ program which takes as input a dated species tree S and a gene tree G in the Newick format, and computes a reconciliation scenario for G and S. Available at http://mbb.univ-montp2.fr/MBB/download_sources/16__TERA 2 publications in the database mention Program TERA

Program TerminusEst

TerminusEst is a Java program which takes as input two rooted (not necessarily binary) trees and outputs their hybridization network in DOT and eNewick format, or simply their hybridization number. It is available at https://skelk.sdf-eu.org/terminusest/ 2 publications in the database mention Program TerminusEst

Program Treeduce

Treeduce is a Java program which takes as input a set of rooted trees, non necessarily binary, and which outputs a reduced version of these trees. These reduced trees will have the same hybridization number (a measure of the complexity of the optimal network which contains all those trees) than the original ones. Available at https://leovaniersel.wordpress.com/software/treeduce/. 2 publications in the database mention Program Treeduce

Program TreeFix-DTL

TreeFix-DTL is a software which takes as input a species tree, as well as sequences of a gene family, to estimate a gene tree for this family, with an optimal recombination scenario. Available at http://compbio.mit.edu/treefix-dtl/ 1 publication in the database mentions Program TreeFix-DTL

Program TreeMix

TreeMix builds a population tree and network from allele frequency data. It is available at http://treemix.googlecode.com/ 1 publication in the database mentions Program TreeMix

Program Treevolve

Treevolve simulates the evolution of DNA sequences under a coalescent model, which allows exponential population growth, population subdivision according to an island model, migration and recombination. It was available at http://evolve.zps.ox.ac.uk/software.html?id=treevolve and can now be found at http://moais.imag.fr/membres/vincent.danjean/deb.html#treevolve> 2 publications in the database mention Program Treevolve

Program TriLoNet

TriLoNet is a Java software package created to construct rooted level-1 phylogenetic networks from aligned DNA sequence data, or from a dense collection of trinets. Available at https://www.uea.ac.uk/computing/TriLoNet 2 publications in the database mention Program TriLoNet

Program TripNet

TripNet is a Java program to compute a phylogenetic network from a triplet set. Version 1.0 is available at https://launchpad.net/tripnet, version 1.1 at https://github.com/azinazadi/TripNet and later versions at http://bioinf.cs.ipm.ir/softwares/tripnet/. 5 publications in the database mention Program TripNet

Program ultra-Net

ultraNet is an ANSI C program which takes as input two or more rooted phylogenetic trees at the Newick format and outputs a rooted phylogenetic network containing them at the eNewick format. It is available at http://rnc.r.dendai.ac.jp/ultraNet.html 1 publication in the database mentions Program ultra-Net

Program Ultranet

Available at http://www.dei.unipd.it/~ciompin/main/Ultranet/Ultranet.html 1 publication in the database mentions Program Ultranet

Program WeakHierarchies

This C++ program computes weak hierarchies from a dissimilarity matrix (available at http://www.info2.uqam.ca/~makarenv/software/Weak_Hierarchies.cpp). 2 publications in the database mention Program WeakHierarchies

Program Xscape

Xscape is a set of Python tools for maximum parsimony phylogenetic event-based tree reconciliation in undated trees using the duplication-loss-transfer model, with applications to gene trees and species trees; parasite trees and host trees; and species trees and area cladograms. Available at http://www.cs.hmc.edu/~hadas/xscape/ 1 publication in the database mentions Program Xscape