The reconstruction of the organization of ancestral genomes is a long-standing problem, motivated by several applications in comparative genomics (Pennisi, 2005). It has received a renewed interest during the past few years, due, among others, to the increasing number of…
Web app
Maximum Likelihood… Maximum Likelihood for Gene Order Analysis

MLGO Maximum Likelihood for Gene Order Analysis

A web tool for the reconstruction of phylogeny and/or ancestral genomes from…

A web tool for the reconstruction of phylogeny and/or ancestral genomes from gene-order data. MLGO was designed for analysis of large-scale genomic changes including not only rearrangements but also…

Desktop app
ProCARs ProCARs

ProCARs

Reconstructs ancestral gene orders as contiguous ancestral regions (CARs) with…

Reconstructs ancestral gene orders as contiguous ancestral regions (CARs) with a progressive homology-based method. ProCARs runs from a phylogeny tree (without branch lengths needed) with a marked…

Desktop app
Parsimonious… Parsimonious Ancestral Reconstruction And Network…

PARANA Parsimonious Ancestral Reconstruction And Network Analysis

Performs parsimony based inference of ancestral biological networks. Given…

Performs parsimony based inference of ancestral biological networks. Given multiple extant networks and phylogenetic information relating extant nodes, PARANA finds a parsimonious set of ancestral…

Desktop app
inferCars inferCars

inferCars

Reconstructs contiguous regions of an ancestral genome. Given information about…

Reconstructs contiguous regions of an ancestral genome. Given information about adjacencies between conserved segments in each modern species, our goal is to infer segment order in the ancestral…

Desktop app
reconstructing… reconstructing ANcestral GEnomeS maps

ANGES reconstructing ANcestral GEnomeS maps

A suite of Python programs that allows reconstructing ancestral genome maps…

A suite of Python programs that allows reconstructing ancestral genome maps from the comparison of the organization of extant-related genomes. ANGES can reconstruct ancestral genome maps for…

Desktop app
Gapped Adjacencies Gapped Adjacencies

GapAdj Gapped Adjacencies

A synteny-based method that is flexible enough to handle a model of evolution…

A synteny-based method that is flexible enough to handle a model of evolution involving whole genome duplication events, in addition to rearrangements, gene insertions, and losses. Ancestral…

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