Phylogeny Reconstruction

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

Found 59 links

Displaying 15 links

ArchaeopteryxTool Content

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Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees.

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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CoPAPTool Content

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CoPAP (Co-evolution of Presence-Absence Patterns) webserver allows inference of co-evolving characters (genes, restriction sites, introns, indels, methylation sites) as manifested by co-occurring gains and losses.

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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

CRISPRcomparTool Content

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Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements are used in CRISPRcompar as a genetic marker for comparative and evolutionary analysis of closely related bacterial strains.

EvoCorTool Content

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EvoCor is a web server for predicting functionally related genes using phylogenetic and expression profiles.

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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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ITS2Tool Content

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The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.

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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MaxAlignTool Content

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MaxAlign is a web server for maximizing usable data in an alignment. It maximizes the number of nucleotide (or amino acid) symbols present in gap-free columns by selecting the optimal subset of sequences to exclude from the alignment.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
MaxAlign: maximizing usable data in an alignment20079

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