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Search found 162 results for « phylogeny »

CSI Phylogeny
Web

CSI Phylogeny Call SNPs & Infer Phylogeny

Identifies variations in whole genome sequencing (WGS) reads and conducts…

Identifies variations in whole genome sequencing (WGS) reads and conducts phylogenetic analysis of isolates. CSI Phylogeny is a webserver which calls and filters the single nucleotide polymorphisms…

UPP
Desktop

UPP Ultra-large alignments using Phylogeny-aware Profiles

Addresses the problem of alignment of very large datasets, potentially…

Addresses the problem of alignment of very large datasets, potentially containing fragmentary data. UPP can align datasets with up to 1,000,000 sequences. UPP produces highly accurate alignments for…

REALPHY
Desktop
Web

REALPHY Reference sequence Alignment-based Phylogeny builder

Aligns raw short-sequence reads to one or more reference sequences. REALPHY can…

Aligns raw short-sequence reads to one or more reference sequences. REALPHY can successfully avoid biases from mapping to a single reference by implementing a procedure for merging alignments…

rRNA phylogeny
Desktop

rRNA phylogeny

Allows phylogenetic analyses (using Phylip) of ribosomal RNA (rRNA). rRNA…

Allows phylogenetic analyses (using Phylip) of ribosomal RNA (rRNA). rRNA phylogeny uses a matrix of empirical substitution rates and the OTRNA model. This method allows to obtain a large number of…

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BitPhylogeny
Desktop

BitPhylogeny

A probabilistic framework to reconstruct intra-tumor evolutionary pathways. The…

A probabilistic framework to reconstruct intra-tumor evolutionary pathways. The statistical model is based on simultaneously assigning markers of evolution to clones, which are represented as both…

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RADIS
Desktop

RADIS analysis of RAD-seq data for InterSpecific phylogeny

Automates and standardizes the analyses of RAD-seq data for phylogenetic…

Automates and standardizes the analyses of RAD-seq data for phylogenetic inference. Users of RADIS can let their raw Illumina data be processed up to phylogenetic tree inference, or stop (and…

PHYLIP
Desktop

PHYLIP the PHYLogeny Inference Package

A free package of programs for inferring phylogenies. It can infer phylogenies…

A free package of programs for inferring phylogenies. It can infer phylogenies by parsimony, compatibility, distance matrix methods, and likelihood. It also computes consensus trees, compute…

Geptop
Desktop
Web

Geptop A Gene essentiality prediction tool for COMPLETE-GENOME based on orthology and phylogeny

A universal approach and tool, based on orthology and phylogeny, to offer gene…

A universal approach and tool, based on orthology and phylogeny, to offer gene essentiality annotations. Compared with the essential genes uniquely identified by the lethal screening, the essential…

Cichlid…
Dataset

Cichlid phylogeny search tool

Contains data of the evolutionary relationship of each cichlid protein to its…

Contains data of the evolutionary relationship of each cichlid protein to its nearest human and zebrafish protein. Cichlid phylogeny search tool can help cichlid researchers to predict biological and…

Simple…
Web

Simple Phylogeny

Provides access to phylogenetic tree generation methods from the ClustalW2…

Provides access to phylogenetic tree generation methods from the ClustalW2 package. Simple Phylogeny is an online method to perform basic phylogenetic analysis on a multiple sequence alignment. It…

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Mitochondrial…
Desktop

Mitochondrial Ontogenetic Phylogeny Estimation

Allows users to choose the ontogenetic processes to place in the ontogenetic…

Allows users to choose the ontogenetic processes to place in the ontogenetic phylogeny. mope is an useful solution to study the dynamics of cancer evolution, or heterogeneous progression in samples…

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CITUP
Desktop

CITUP Clonality Inference in Tumors Using Phylogeny

A combinatorial method that infers clonal populations and their frequencies…

A combinatorial method that infers clonal populations and their frequencies while satisfying phylogenetic constraints and is able to exploit data from multiple samples. Using simulated datasets and…

MetaPiga
Desktop

MetaPiga phylogeny inference using the Metapopulation genetic algorithm

Aims users to improve the rapidity in building maximum likelihood (ML) trees.…

Aims users to improve the rapidity in building maximum likelihood (ML) trees. MetaPiga is able to provide visualization and statistical analyses of trees. The algorithm can also run a rapid…

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SPRUCE
Desktop

SPRUCE Somatic Phylogeny Reconstruction Using Combinatorial Enumeration

Infers a multi-state perfect phylogeny describing the evolutionary history of…

Infers a multi-state perfect phylogeny describing the evolutionary history of the somatic mutations (Single-Nucleotide Variations (SNV)s and Copy-Number Aberrations (CNAs)) of a tumor given…

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MixedPerfectPhy…
Desktop

MixedPerfectPhylogeny

Contains methods for the MINIMUM CONFLICT-FREE ROW SPLIT problem.…

Contains methods for the MINIMUM CONFLICT-FREE ROW SPLIT problem. MixedPerfectPhylogeny assembles the implementations of two algorithms: an efficient heuristic algorithm based on coloring…

PhyloJIVE
Web

PhyloJIVE Phylogeny Javascript Information Visualiser and Explorer

A web-based application that integrates biodiversity information aggregated…

A web-based application that integrates biodiversity information aggregated from many sources with phylogenetic trees. PhyloJIVE demonstrates that it is possible and useful to assemble interactive…

AnGST
Web

AnGST ANalyzer of Gene and Species Trees

Allows analysis of gene and species trees. AnGST is a phylogenomic method…

Allows analysis of gene and species trees. AnGST is a phylogenomic method comparing individual gene phylogenies with the phylogeny of organisms. This tool uses the topology of the genealogy tree to…

CGD
Dataset

CGD Candida Genome Database

Provides gene, protein and sequence information for multiple Candida species.…

Provides gene, protein and sequence information for multiple Candida species. CGD contains web-based tools for accessing, analyzing and exploring these data, to facilitate and accelerate research…

ADAPTML
Web

ADAPTML

Allows identification of populations as groups of related strains sharing a…

Allows identification of populations as groups of related strains sharing a common projected habitat, which reflects their relative abundance in the measured environmental categories. ADAPTML maps…

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ConStrains
Desktop

ConStrains Conspecific Strains

An open-source algorithm that identifies conspecific strains from metagenomic…

An open-source algorithm that identifies conspecific strains from metagenomic sequence data and reconstructs the phylogeny of these strains in microbial communities. ConStrains uses single-nucleotide…

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