Phylogeny Reconstruction

This section contains links to tools and databases for phylogeny reconstruction, including taxonomy resources

Found 60 links

Displaying 15 links

Berkeley Phylogenomics GroupTool Content

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The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

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Bioinformatics ToolkitTool Content

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This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.

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CIPResTool Content

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The Cyberinfrastructure for Phylogenetic Research (CIPRes) project aims to develop a computational infrastructure for systematics. Other goals of the project include providing a central resource enabling computational systematics and education and training initiatives. The website also contains a substantial list of links to related software.

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ConSeqTool Content

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ConSeq is a tool for predicting functionally and structurally important amino acid residues in protein sequences. The predictions are based on the assumptions that residues of functional importance are often conserved and solvent-accessible, and those of structural importance are often conserved and located in the protein core. A multiple sequence alignment is used to predict the relative solvent accessibility state and the evolutionary rate at each residue. ConSeq has been integrated into ConSurf (2010).

cpnDBDatabase Content

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cpnDB is a curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. cpnDB is built and maintained with open source tools.

links directory index: 73
TitlePublication YearGoogle Scholar Citation Count
cpnDB: a chaperonin sequence database200473

CVTreeTool Content

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Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.

d-OmixTool Content

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A Mixer of Protein Domain Analysis Tools (d-Omix) provides tools to analyze, compare and visualize protein data sets with respect to their combinations of protein domains.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
d-Omix: a mixer of generic protein domain analysis tools20091

DichroMatchTool Content

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DichroMatch webserver identifies proteins with similar spectral characteristics as a way to detect possible structurally and functionally related proteins and homologues. Users input a query spectrum which is searched against the protein circular dichromism data bank or a user provided data set.

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EvolViewTool Content

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EvolView is a web server for displaying, managing and customizing phylogenetic trees.

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FastMLTool Content

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FastML is a webserver for computing and reconstructing ancestral sequences using maximum likelihood.

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iTOLTool Content

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The Interactive Tree of Life (iTOL) tool is useful for the display, manipulation and annotation of phylogenetic trees. In addition to standart tree viewer functions, it offers powerful annotation of phylogenetic trees with various additional datasets. Annotated trees can be exported into various graphical formats. An user account system is provided, offering easy tree management and sharing through workspaces and projects. Programmatic access is also available.

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Joes Site - Phylogeny ProgramsResource Content

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Comprehensive list of phylogeny packages, compiled by Joe Felsenstein, creator of Phylip.

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