Phylogenomic analysis software tools and databases

Phylogenomics steps

Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and the demographic changes and migration patterns of species. The advancement of sequencing technologies has taken…

Phylogenomic analysis software tools and databases

Most Recent Tools

MPR
Desktop

MPR Most Parsimonious Reconciliation

Considers duplications, transfers and losses of genes. MPR yields a fast and…

Considers duplications, transfers and losses of genes. MPR yields a fast and exact algorithm to infer time consistent and most parsimonious reconciliations. It optimizes a parsimony criterion…

SPIDIR
Desktop

SPIDIR Species Informed Distance-based Reconstruction

Reconstructs gene-tree by using learning gene- and species-specific…

Reconstructs gene-tree by using learning gene- and species-specific substitution rates across multiple complete genomes. SPIDIR achieves significantly higher accuracy, addresses the species-level…

DLCpar
Desktop

DLCpar

Infers a most parsimonious (MP) history of a gene family in the presence of…

Infers a most parsimonious (MP) history of a gene family in the presence of duplications, losses, and incomplete lineage sorting (ILS). DLCpar relies on a reconciliation structure, the labeled…

auspice
Desktop

auspice

Gives an interactive display of inferences produced by augur pipeline. Auspice…

Gives an interactive display of inferences produced by augur pipeline. Auspice is a part of the nextstrain project. The nextstrain project derives from nextflu, which was specific to influenza…

Most Popular Tools

PhyloPat
Data

PhyloPat

Allows the complete Ensembl gene database to be queried using phylogenetic…

Allows the complete Ensembl gene database to be queried using phylogenetic patterns. PhyloPat offers the possibility of querying with binary phylogenetic patterns or regular expressions, or through a…

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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