• ecceTERA

  • Referenced in 6 articles [sw24891]
  • undated, fully dated or partially dated species trees. The ecceTERA reconciliation model and algorithm generalize ... most published DTL parsimony algorithms for binary species trees and binary gene trees. Moreover, ecceTERA...
  • TxT

  • Referenced in 1 article [sw07679]
  • binary gene tree and binary species tree Tree reconciliation approach to inferring the duplication history ... problems when input gene and species trees are non-binary. We present the first linear ... binary gene tree and a binary species tree that minimizes the gene loss cost under ... method for reconciling two non-binary trees, this algorithm has been implemented in a software...
  • phytools

  • Referenced in 14 articles [sw10003]
  • phylogenetic analysis of comparative data from species. For example, the package includes functions for Bayesian ... rate of character evolution on the tree; fast Brownian motion simulation and simulation under several ... trait evolution; fitting a model of correlated binary trait evolution; locating the position...
  • OCTAL

  • Referenced in 2 articles [sw29609]
  • contain all of the species of interest. As incomplete gene trees can impact downstream analyses ... completion of gene trees is desirable. Results: We introduce the Optimal Tree Completion problem ... problem that involves completing an unrooted binary tree (i.e., adding missing leaves ... minimize its distance from a reference tree on a superset of the leaves. We present...
  • GATC

  • Referenced in 1 article [sw29603]
  • with a species tree to correct, a posteriori, errors in gene trees inferred from multiple ... GATC, a new algorithm for reconstructing a binary gene tree with branch length. GATC returns...
  • GAP

  • Referenced in 3189 articles [sw00320]
  • GAP is a system for computational discrete algebra...
  • Gerris

  • Referenced in 344 articles [sw00341]
  • Gerris is a Free Software program for the...
  • gmp

  • Referenced in 282 articles [sw00363]
  • GMP is a free library for arbitrary precision...
  • Magma

  • Referenced in 3315 articles [sw00540]
  • Computer algebra system (CAS). Magma is a large...
  • Maple

  • Referenced in 5373 articles [sw00545]
  • The result of over 30 years of cutting...
  • Mathematica

  • Referenced in 6355 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 13544 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • nauty

  • Referenced in 609 articles [sw00611]
  • graph-theoretic program NAUTY: nauty is a program...
  • R

  • Referenced in 9969 articles [sw00771]
  • R is a language and environment for statistical...
  • SageMath

  • Referenced in 1994 articles [sw00825]
  • Sage (SageMath) is free, open-source math software...
  • SINGULAR

  • Referenced in 1508 articles [sw00866]
  • SINGULAR is a Computer Algebra system (CAS) for...
  • TSPLIB

  • Referenced in 698 articles [sw00983]
  • TSPLIB is a library of sample instances for...
  • Cayley

  • Referenced in 131 articles [sw01053]
  • An introduction to the Group Theory Language, Cayley...
  • AUTO

  • Referenced in 943 articles [sw01059]
  • AUTO is a software for continuation and bifurcation...
  • GLIM

  • Referenced in 193 articles [sw01126]
  • GLIM - a system for interactive fitting of generalized...