Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Unclassified tools | Phylogenomics

STELLS2
Desktop

STELLS2

Computes the gene tree probability. STELLS2 is usually more accurate than…

Computes the gene tree probability. STELLS2 is usually more accurate than several existing methods when there is one allele per species. It outperforms these methods significantly when there are…

node dating
Desktop

node dating

Estimates the dates of the internal nodes of a phylogenetic tree. node.dating…

Estimates the dates of the internal nodes of a phylogenetic tree. node.dating is a divergence-time analysis software and uses a maximum-likelihood method. It can be extended to incorporate a variable…

PANDIT
Dataset

PANDIT Protein and Associated Nucleotide Domains with Inferred Trees

Assists researchers to investigate molecular evolutionary phenomena and to…

Assists researchers to investigate molecular evolutionary phenomena and to develop phylogenetic and comparative genomic methodology. PANDIT provides a set of aligned protein coding sequences, both at…

RogueNaRok
Desktop

RogueNaRok

Allows identification of rogue taxon. RogueNaRok is an algorithm that…

Allows identification of rogue taxon. RogueNaRok is an algorithm that implements the maximum agreement subtree, the triple frequency, and node distance methods as well as a tool for pruning taxa from…

SplitSup
Desktop

SplitSup

Computes split scores. SplitSup is a code reads an alignment in PHYLIP format…

Computes split scores. SplitSup is a code reads an alignment in PHYLIP format and returns either (i) a set of scores corresponding to a list of user-provided splits; or (ii) the values of a split…

ClonalOrigin
Desktop

ClonalOrigin

Allows to work about the history of recombination events that affected a given…

Allows to work about the history of recombination events that affected a given sample of bacterial genomes. ClonalOrigin run on as comparative analysis of sequences of a sample of bacterial genomes…

LSX
Desktop

LSX Locus Specific Sequence Subsampling

Reduces lineage evolutionary rate heterogeneity gene-by-gene in multi-gene…

Reduces lineage evolutionary rate heterogeneity gene-by-gene in multi-gene datasets. LSX is effective in reducing long branch attraction (LBA) artefacts in simulated nucleotide data and in two…

P4P
Web

P4P Peptidomes for Phylogenies

Enables the in silico inference of bacterial taxonomy through the analysis of…

Enables the in silico inference of bacterial taxonomy through the analysis of peptidomes. The P4P methodology uses whole genome data and in silico protein digestion to infer bacterial taxonomy,…

Phylesystem
Desktop

Phylesystem

Provides a git-based data store for archiving and curating phylogenetic…

Provides a git-based data store for archiving and curating phylogenetic estimates of species relationships. By incorporating curation into the data storage, Phylesystem have lowered the activation…

ClonalFrameML
Desktop

ClonalFrameML

Uses maximum likelihood inference to simultaneously detect recombination in…

Uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction. ClonalFrameML can analyse hundreds of genomes in a…

ITIS
Dataset

ITIS Integrated Taxonomic Information System

Provides a repository for taxonomic data. ITIS is an authoritative source,…

Provides a repository for taxonomic data. ITIS is an authoritative source, result of a partnership of federal US agencies, of currently used names of all biological taxa. It proposes guidelines and…

PhyloSort
Desktop

PhyloSort

Permits inspection of the topology and other aspects of large sets of…

Permits inspection of the topology and other aspects of large sets of phylogenetic trees in a phylogenomic context. PhyloSort is able to quantify the number of genes or trees that support different…

physamp
Desktop

physamp Phylogenetic Sampling and Optimization of sequence alignments

Concerns especially phylogenetic sampling. physamp takes into account of…

Concerns especially phylogenetic sampling. physamp takes into account of phylogenetic tree to sample a sequence alignment. This tool contains two programs: (1) bppalnoptim that samples a sequence…

SPIMAP
Desktop

SPIMAP Species Informed Maximum A Posteriori Gene Tree Reconstruction

Provides a phylogenetic reconstruction method specifically designed for…

Provides a phylogenetic reconstruction method specifically designed for reconstructing gene trees in the case of a known species tree. SPIMAP uses a Bayesian framework to model sequence evolution,…

SCOTTI
Desktop

SCOTTI Structured COalescent Transmission Tree Inference

Models each host as a distinct population, and transmissions between hosts as…

Models each host as a distinct population, and transmissions between hosts as migration events. This phylogenetic software can (i) infer transmission events, (ii) account for the uncertainty…

OpenMEE
Desktop

OpenMEE

Assists is carrying out and teaching meta-analysis in Ecology and Evolutionary…

Assists is carrying out and teaching meta-analysis in Ecology and Evolutionary biology (E&E). OpenMEE was developed to make advanced methods for statistical research synthesis, based on best…

Bio::Phylo
Desktop

Bio::Phylo

Allows users to handle rich phylogenetic data objects. Bio::Phylo is composed…

Allows users to handle rich phylogenetic data objects. Bio::Phylo is composed of over 50 modules which authorize several functionalities in manipulating and transforming objects such as annotation,…

HiMAP
Desktop

HiMAP Highly Multiplexed Amplicon-based Phylogenomics

Produces phylogenomic datasets using highly multiplexed amplicon sequencing.…

Produces phylogenomic datasets using highly multiplexed amplicon sequencing. HiMAP employs amplicon sequencing based on highly multiplexed polymerase chain reaction (PCR) to generate its datasets. It…

SwissTree
Dataset

SwissTree

Gathers high-confidence model gene trees for the benchmarking of inferred gene…

Gathers high-confidence model gene trees for the benchmarking of inferred gene relationships. SwissTree aims to build a reproducible and coherent system for reference gene tree curation. Moreover,…

STRIDE
Desktop

STRIDE Species Tree Root Inference from gene Duplication Events

Identifies sets of well-supported gene duplication events from cohorts of gene…

Identifies sets of well-supported gene duplication events from cohorts of gene trees. STRIDE is an algorithm developed to analyze these duplication events to infer a probability distribution over an…

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…

MAP-DP
Desktop

MAP-DP

Factorizes branch lengths into time and rates. MAP-DP is a Bayesian framework…

Factorizes branch lengths into time and rates. MAP-DP is a Bayesian framework easily adapted to take divergence time information into account, by restricting a speciation to a specific interval or…

tqDist
Desktop

tqDist

Computes the triplet and quartet distances between general rooted or unrooted…

Computes the triplet and quartet distances between general rooted or unrooted trees, respectively. The tqDist program is based on algorithms with running time O(n log n) for the triplet distance…

TimeTree
Dataset

TimeTree

Offers a public knowledge-base for information on the tree-of-life and its…

Offers a public knowledge-base for information on the tree-of-life and its evolutionary timescale. TimeTree is a web-based resource for researchers and educators from all fields of science to assist…

STARRInIGHTS
Desktop
GenomeInfoDbDat…
Dataset

GenomeInfoDbData

Contains files for mapping between NCBI taxonomy ID and species.…

Contains files for mapping between NCBI taxonomy ID and species. GenomeInfoDbData is applicable to functions in the GenomeInfoDb package.

TreeBASE
Dataset

TreeBASE

Provides information about phylogenetic trees and the data used to generate…

Provides information about phylogenetic trees and the data used to generate them. TreeBASE takes a census of 4,076 publications. Available studies provides 8,233 matrices and resulted in 12,817 trees…

Actinobase
Dataset

Actinobase

Collects information about the diversity and functional analysis of salt…

Collects information about the diversity and functional analysis of salt tolerant alkaliphilic actinomycetes. Actinobase compiles data from over 40 alkaliphilic actinomycetes including respect to…

SaguaroGW
Desktop

SaguaroGW Saguaro Genome-Wide

Detects signatures of selection within populations, strains, or species.…

Detects signatures of selection within populations, strains, or species. Saguaro identifies regions under lineage-specific constraint for the first set, and genomic segments that we attribute to…

MicroFootPrinte…
Web

MicroFootPrinter

Assists in discovering phylogenetic footprinting of novel cis-regulatory…

Assists in discovering phylogenetic footprinting of novel cis-regulatory elements in prokaryotic genomes. MicroFootPrinter provides microbiologists with a convenient front end for FootPrinter,…

CDAO-Store
Web

CDAO-Store Comparative Data Analysis Ontology Store

Provides a web interface for a semantic-based repository of phylogenetic data.…

Provides a web interface for a semantic-based repository of phylogenetic data. CDAO-Store is an open source platform which offers three modules: (i) a data importer module for importing phylogenies…

ELKUType
Dataset

ELKUType

Compiles type specimens conserved in the Entomological Laboratory of Kyushu…

Compiles type specimens conserved in the Entomological Laboratory of Kyushu University (Japan). The ELKUType focuses on holotypes. Searches can be made by a simple logical formula or by a…

GeneTrees
Dataset

GeneTrees

Provides evolutionary models for all genomic components of fully sequenced…

Provides evolutionary models for all genomic components of fully sequenced bacterial genomes describing the pattern of common ancestry observed among sequences. GeneTrees is a phylogenomics analysis…

FGF
Web

FGF Fishing Gene Family

Integrates homologous search and evolutionary analysis. FGF is a web server…

Integrates homologous search and evolutionary analysis. FGF is a web server that uses protein sequences as bait for fishing gene families and extracting related information. It permits to visualize…

DED
Dataset

DED Database of Evolutionary Distances

Contains sequence information from several vertebrate species clustered into…

Contains sequence information from several vertebrate species clustered into homology groups. DED is an online resource for gene function assignment, molecular phylogenetic studies, search for…

G T A T C G C T A
InvChecker
Desktop

InvChecker

Detects inversions in the cystic fibrosis transmembrane conductance regulator…

Detects inversions in the cystic fibrosis transmembrane conductance regulator (CFTR) region. InvChecker uses microinversions as evolutionary characters to reconstruct phylogeny. The software defines…

CONSEL
Desktop

CONSEL

Allows evaluation of the confidence of phylogenetic tree selection. CONSEL…

Allows evaluation of the confidence of phylogenetic tree selection. CONSEL provides features to read the matrix of the site-wise log-likelihoods of the candidate trees. It can be applied to…

xREI
Web

xREI

Allows exploration of a range of pre-defined phylo-grammars and provides tools…

Allows exploration of a range of pre-defined phylo-grammars and provides tools for visualization of user’s phylo-grammars. xREI is a web server that provides a method for visualizing phylo-grammars…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.