• PANTHER

  • Referenced in 15 articles [sw22973]
  • with particular genes in the common ancestral genomes of extant species...
  • INDELible

  • Referenced in 8 articles [sw23043]
  • alignment, phylogenetic tree inference, and ancestral sequence, or genome reconstruction...
  • ANGES

  • Referenced in 1 article [sw29622]
  • ANGES: reconstructing ANcestral GEnomeS maps. Summary: ANGES is a suite of Python programs that allows ... reconstructing ancestral genome maps from the comparison of the organization of extant-related genomes. ANGES ... reconstruct ancestral genome maps for multichromosomal linear genomes and unichromosomal circular genomes. It implements methods ... cereal, amniote, yeast or bacteria ancestral genomes are provided, computed with ANGES. Availability: ANGES...
  • MLGO

  • Referenced in 2 articles [sw29621]
  • ancestral inference from gene-order data. Background: The rapid accumulation of whole-genome data ... gene-order data for phylogenetic analyses and ancestral reconstruction. Current software and web servers typically ... reconstruction of phylogeny and/or ancestral genomes from gene-order data. MLGO is based on likelihood...
  • Mercator

  • Referenced in 1 article [sw23116]
  • from the same region in an ancestral genome. However, it has been pointed out that ... regions within each genome and hypothetical ancestral genome. Maps listing these relationships are extremely valuable...
  • GASTS

  • Referenced in 5 articles [sw29624]
  • trees up to 100 taxa and genomes of up to 10,000 syntenic blocks. GASTS ... unapproachable problems, such as accurate ancestral reconstruction of large genomes and phylogenetic inference for high...
  • PoMo

  • Referenced in 8 articles [sw35039]
  • phylogenetic trees for individual genes or genomic segments. If these incongruencies are not accounted ... simple maximum likelihood approach that accounts for ancestral variation and incomplete lineage sorting ... show that PoMo is well suited for genome-wide species tree estimation and that...
  • ProCARs

  • Referenced in 1 article [sw29623]
  • context of ancestral gene order reconstruction from extant genomes, there exist two main computational approaches ... detection of a set of potential ancestral contiguity features, followed by the assembling of these...
  • FlatNJ

  • Referenced in 1 article [sw20300]
  • genome sequences, where recombination has taken place, fluorescent proteins in corals, where ancestral sequences...
  • SABER

  • Referenced in 4 articles [sw33848]
  • SABER is a program suitable for genome-scale data which uses a “Markov-hidden Markov ... This local ancestry is referred to as “ancestral blocks”. Like HAPMIX, it models the ancestral...
  • HapMix

  • Referenced in 6 articles [sw33847]
  • unlinked markers; but, using all markers from genome-wide scanning arrays, it should in principle ... utility for inferring ancestry, learning about ancestral populations, and inferring dates of admixture. We validate...
  • LEA

  • Referenced in 1 article [sw25208]
  • analyses of population structure and genome scans for local adaptation. It includes statistical methods ... genotypic matrices and evaluating the number of ancestral populations (snmf, pca); and identifying genetic polymorphisms...
  • MALDsoft

  • Referenced in 1 article [sw33852]
  • proportions at a locus deviate from the genome average. Our power calculations show that ... allele frequencies are substantially different in the ancestral populations, the power of admixture mapping...
  • iMOT

  • Referenced in 1 article [sw32855]
  • proteins sharing similar folds and possessing common ancestral lineage. Spatial interactions between conserved stretches ... homologies among the largely unassigned sequences in genome databases. Information on such motifs should also...
  • Mathematica

  • Referenced in 6445 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • R

  • Referenced in 10196 articles [sw00771]
  • R is a language and environment for statistical...
  • SageMath

  • Referenced in 2033 articles [sw00825]
  • Sage (SageMath) is free, open-source math software...
  • SINGULAR

  • Referenced in 1522 articles [sw00866]
  • SINGULAR is a Computer Algebra system (CAS) for...
  • TSPLIB

  • Referenced in 711 articles [sw00983]
  • TSPLIB is a library of sample instances for...