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Phylogenomic analysis software tools and databases

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…

Phylogenomics steps

Most recent bioinformatics tools

SaffronTree
Desktop

SaffronTree

Allows the construction of a tree directly from raw reads or from assembled…

Allows the construction of a tree directly from raw reads or from assembled sequences. SaffronTree utilizes a kmer analysis to construct a phylogenetic neighbor joining tree in newick format. This…

QuickTree
Desktop

QuickTree

Allows users to reconstruct phylogenies for very large protein families.…

Allows users to reconstruct phylogenies for very large protein families. QuickTree is a program simplifying activities such as bootstrapping and the investigation of more sophisticated distance…

SDM
Web

SDM Super Distance Matrix

Transforms the source matrices without modifying their topological message to…

Transforms the source matrices without modifying their topological message to create phylogenies from large sets of homologous gene. SDM brings the source matrices as close as possible to each other.…

AncestralAge
Desktop

AncestralAge

Calculates phylogenetic divergence time in a reduced time way. AncestralAge…

Calculates phylogenetic divergence time in a reduced time way. AncestralAge increases the speed thanks to different methods: algorithmic improvements, approximation methods, and parallelization of…

Most popular analytical software and databases

EvolView
Web

EvolView

A comprehensive web application for visualizing, annotating and managing…

A comprehensive web application for visualizing, annotating and managing phylogenetic trees. Evolview allows users to visualize phylogenetic trees in various formats, customize the trees through…

PhyloPat
Dataset

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…

RAxML
Desktop

RAxML Randomized Axelerated Maximum Likelihood

A popular program for phylogenetic analyses of large datasets under maximum…

A popular program for phylogenetic analyses of large datasets under maximum likelihood.

MEGA
Desktop

MEGA Molecular Evolutionary Genetics Analysis

An integrated tool for conducting sequence alignment, inferring phylogenetic…

An integrated tool for conducting sequence alignment, inferring phylogenetic trees, estimating divergence times, mining online databases, estimating rates of molecular evolution, inferring ancestral…

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