• PhyloNetwork

  • Referenced in 27 articles [sw28216]
  • package and an alignment tool for phylogenetic networks. Phylogenetic networks are a generalization of phylogenetic ... applications to work with phylogenetic networks, none of which are open-source libraries, and they ... allow for the comparative analysis of phylogenetic networks by computing distances between them or aligning ... bundle and implements many algorithms on phylogenetic networks. We have also developed a Java applet...
  • QNet

  • Referenced in 11 articles [sw19662]
  • QNet: a software package for estimating phylogenetic networks based on quartets. QNet is a software ... Java which encompasses methods for generating phylogenetic networks from quartet data, as per the method...
  • T-REX

  • Referenced in 8 articles [sw20724]
  • inferring, validating and visualizing phylogenetic trees and networks. T-REX (Tree and reticulogram REConstruction ... dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal ... Neighbor Joining, NINJA, BioNJ, PhyML, RAxML, random phylogenetic tree generator and some well-known sequence ... allows for validating and visualizing phylogenetic trees and networks which can be built from distance...
  • tcp_package

  • Referenced in 5 articles [sw34266]
  • program for verification of phylogenetic network models. Results: We design an exponential time but efficient ... method for determining whether or not a phylogenetic ... tree is displayed in an arbitrary phylogenetic network. It is developed on the basis ... called reticulation-visible property of phylogenetic networks. Availability and Implementation: A C-program is available...
  • Tanglegrams

  • Referenced in 4 articles [sw21231]
  • Tanglegrams for rooted phylogenetic trees and networks. MOTIVATION: In systematic biology, one is often faced ... with the task of comparing different phylogenetic trees, in particular in multi-gene analysis ... increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly ... definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach for computing...
  • S-Cluster++

  • Referenced in 2 articles [sw29662]
  • solving the cluster containment problem for phylogenetic networks. Motivation: Comparative genomic studies indicate that extant ... This has motivated biologists to use phylogenetic networks and other general models to study genome ... algorithmic problems arising from verification of phylogenetic networks and from computing Robinson-Foulds distance ... space of phylogenetic networks are the tree and cluster containment problems. The former asks...
  • MURPAR

  • Referenced in 2 articles [sw29666]
  • fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees. Phylogenetic networks provide ... transfer (HGT). One approach for inferring phylogenetic networks is based on reconciling gene trees, assuming ... been introduced to construct and analyze phylogenetic networks. Here, we address the computational problem ... inferring phylogenetic networks with minimum reticulations from a collection of gene trees. As this problem...
  • PhyloNetworks

  • Referenced in 2 articles [sw29667]
  • PhyloNetworks: a package for phylogenetic networks. PhyloNetworks is a Julia package for the inference, manipulation ... visualization, and use of phylogenetic networks in an interactive environment. Inference of phylogenetic networks ... hybrid node support. Networks can be used for phylogenetic comparative analysis of continuous traits...
  • IcyTree

  • Referenced in 2 articles [sw25096]
  • rapid browser-based visualization for phylogenetic trees and networks. Summary: IcyTree is an easy ... visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist ... having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently ... zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible. Availability...
  • phangorn

  • Referenced in 6 articles [sw08311]
  • analysis in R (Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, Distance...
  • NetDiversity

  • Referenced in 1 article [sw24766]
  • Phylogenetic diversity and biodiversity indices on phylogenetic networks. In biodiversity conservation it is often necessary ... evolution is not treelike and thus, phylogenetic networks have been developed as a generalization ... diversity indices from phylogenetic trees to phylogenetic networks. On the one hand, we consider ... treelike content of a phylogenetic network, e.g. the (multi)set of phylogenetic trees displayed...
  • metafor

  • Referenced in 31 articles [sw12291]
  • Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic...
  • Phylonets

  • Referenced in 1 article [sw18581]
  • child cluster networks. In general, a phylogenetic network is a graphical representation of an evolutionary ... networks) are a special class of phylogenetic networks that allow to represent evolutionary histories where...
  • TriLoNet

  • Referenced in 1 article [sw36903]
  • level-1 networks. In evolutionary biology, phylogenetic networks are constructed to represent the evolution ... trinet distance between two level-1 networks. Employing simulations, we also present a comparison between ... called Robinson-Foulds phylogenetic network metric restricted to level-1 networks. The algorithms described...
  • phyloXML

  • Referenced in 4 articles [sw35271]
  • language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements...
  • FlatNJ

  • Referenced in 1 article [sw20300]
  • Split networks are a type of phylogenetic network that allow visualization of conflict in evolutionary...
  • Phylogemetric

  • Referenced in 1 article [sw29191]
  • Phylogemetric: A Python library for calculating phylogenetic network metrics. Phylogemetric is a Python library ... Residual (Gray, Bryant, and Greenhill 2010) for phylogenetic data. These methods are used in studies...
  • ARB

  • Referenced in 2 articles [sw17153]
  • linked via local or worldwide networks. A phylogenetic tree visualized in the main window...
  • SplitsTree

  • Referenced in 30 articles [sw12234]
  • number of different and sometimes conflicting phylogenetic signals, and thus do not always clearly support ... data are represented by a tree-like network that may indicate evidence for different...
  • MI-GRAAL

  • Referenced in 3 articles [sw08318]
  • scores for PPI networks of different herpes viruses, we reconstruct their phylogenetic relationship. This ... reconstructed from purely topological alignments of PPI networks...