• MultiLoc2

  • Referenced in 8 articles [sw22456]
  • previous MultiLoc predictor by incorporating phylogenetic profiles and Gene Ontology terms. Two different datasets were ... protein localization prediction system. By incorporating phylogenetic profiles and Gene Ontology terms MultiLoc2 yields higher...
  • DIMA

  • Referenced in 4 articles [sw26868]
  • have been implemented so far: domain phylogenetic profiling and experimentally demonstrated domain contacts from known...
  • TIPP

  • Referenced in 1 article [sw33188]
  • TIPP: taxonomic identification and phylogenetic profiling. We present taxon identification and phylogenetic profiling (TIPP ... taxon identification and abundance profiling method. TIPP combines SAT-enabled phylogenetic placement a phylogenetic placement ... recall, and results in improved abundance profiles. TIPP is highly accurate even in the presence...
  • GeneTRACE

  • Referenced in 1 article [sw35747]
  • that given a set of correct phylogenetic profiles and a correct species tree, ancestral gene ... reconstruction of gene content-based phylogenetic trees, suggesting that these trees may be accurate...
  • FunCoup

  • Referenced in 1 article [sw27475]
  • novel method to incorporate phylogenetic profile similarity. Several datasets have been updated and new data...
  • FastTree

  • Referenced in 9 articles [sw28979]
  • with Profiles instead of a Distance Matrix. FastTree infers approximately-maximum-likelihood phylogenetic trees from...
  • ARB

  • Referenced in 2 articles [sw17153]
  • linked via local or worldwide networks. A phylogenetic tree visualized in the main window ... primary and secondary structure editing, profile and filter calculation, phylogenetic analyses, specific hybridization probe design...
  • PhyloBayes MPI

  • Referenced in 2 articles [sw23042]
  • PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Modeling across ... recognized as important for obtaining more accurate phylogenetic reconstructions. Both finite and infinite mixture models ... Dirichlet process model over equilibrium frequency profiles implemented in PhyloBayes has often been used ... cores, thus allowing faster phylogenetic reconstruction under complex mixture models. PhyloBayes MPI is freely available...
  • RadCon

  • Referenced in 2 articles [sw37016]
  • Macintosh® program for manipulating and analysing phylogenetic trees. The program can determine the Cladistic Information ... produce the strict basic Reduced Cladistic Consensus profile of a set of trees and convert...
  • jpHMM

  • Referenced in 4 articles [sw10925]
  • jpHMM (jumping profile Hidden Markov Model) is a probabilistic approach to compare a sequence ... virus (HBV) genomes. For a query sequence phylogenetic recombination breakpoints are predicted and each region...
  • Canopy

  • Referenced in 0 articles [sw16685]
  • mutation profiles of each subpopulation, and inferring the tumor’s phylogenetic history. The input...
  • NGS

  • Referenced in 1 article [sw29692]
  • reveal the high-resolution whole genome SNP profiles and the structural variants of different isolates ... methicillin-susceptible S. aureus (MSSA) strains. The phylogenetic analysis of whole genomes and particular regions...
  • ATLAS

  • Referenced in 199 articles [sw00056]
  • This paper describes the Automatically Tuned Linear Algebra...
  • 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...
  • R

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

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