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Ancestral genome reconstruction software tools | Phylogenomics

Ancestral sequence reconstruction (ASR) methods require as input both a multiple sequence alignment (MSA) of existing sequences and a corresponding phylogenetic tree (either provided or computed from the MSA). They output a statistical inference of…
MGRA
Web
Desktop

MGRA Multiple Genome Rearrangements and Ancestors

Allows users to reconstruct ancestor genomes and extant genomes evolution. MGRA…

Allows users to reconstruct ancestor genomes and extant genomes evolution. MGRA was firstly developed for study seven mammalians: human, macaque, chimpanzee, mouse, dog, rat and opossum. Genome…

MGR
Desktop
Web

MGR Multiple Genome Rearrangements

Allows users to generate genome-scale phylogenetic tree reconstruction and…

Allows users to generate genome-scale phylogenetic tree reconstruction and deriving ancestral gene orders. MGR is a genome rearrangement algorithm based on the rearrangement distance, applicable to…

Reconstructing…
Desktop
ProCARs
Desktop

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…

SAMedian
Desktop

SAMedian

Provides a method for phylogenetic reconstruction SAMedian calculates the…

Provides a method for phylogenetic reconstruction SAMedian calculates the three-genome median problem thanks to a double-cut-and-join (DCJ) sorting between two genomes combined to a simulated…

FastML
Desktop
Web

FastML

A user-friendly tool for the reconstruction of ancestral sequences. FastML…

A user-friendly tool for the reconstruction of ancestral sequences. FastML implements various novel features that differentiate it from existing tools: (i) FastML uses an indel-coding method, in…

maxAlike
Desktop
Web

maxAlike

Reconstructs a genomic sequence for a specific taxon based on sequence homologs…

Reconstructs a genomic sequence for a specific taxon based on sequence homologs in other species. The input is a multiple sequence alignment and a phylogenetic tree that also contains the target…

MLGO
Web

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…

inferCars
Desktop

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…

ANGES
Desktop

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…

Ancestors
Web

Ancestors

A web server allowing one to easily and quickly perform the last three steps of…

A web server allowing one to easily and quickly perform the last three steps of the ancestral genome reconstruction procedure. Ancestors implements several alignment algorithms, an indel maximum…

ROCOCO
Web
Desktop

ROCOCO Reconstruction Of COnserved COntiguous regions

Rebuilds ancestral gene clusters. ROCOCO determines optimal sets of gene…

Rebuilds ancestral gene clusters. ROCOCO determines optimal sets of gene clusters for the inner nodes from the topology of a phylogenetic tree and the gene orders of the leaf nodes. It provides…

roci
Web

roci

Allows deduction and description of a set of likely ancestral gene orders at…

Allows deduction and description of a set of likely ancestral gene orders at each internal node of a phylogenetic tree with a given topology. Roci consists in operations on sets of conserved…

Cocos
Desktop

Cocos

Constructs phylogenies of multi-domain proteins. With a given species tree and…

Constructs phylogenies of multi-domain proteins. With a given species tree and domain phylogenies, the procedure infers the composition of ancestral multi-domain proteins. Cocos implements and extend…

GASTS
Algorithm

GASTS Generalized Adequate Subtree Tree Scoring

Provides a tree-scoring algorithm by using generalized adequate subgraphs.…

Provides a tree-scoring algorithm by using generalized adequate subgraphs. GASTS intends to furnish accurate values with several practical applications in comparative genomics. The algorithm was…

G T A T C G C T A
MySSP
Desktop

MySSP

Constructs an initial DNA sequence at the root of the tree and simulates…

Constructs an initial DNA sequence at the root of the tree and simulates evolution across the tree using a variety of common models of DNA evolution. MySSP is a program for the simulation of DNA…

PARANA
Desktop

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…

GapAdj
Desktop

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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