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Phylogeny Reconstruction

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

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Found 51 links

Displaying 15 links

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

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.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

Bioinformatics ToolkitTool Content

http://toolkit.tuebingen.mpg.de/

DNA > Annotations
DNA > DNA and Genomic Analysis
DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Localization and Targeting
Protein > Molecular Dynamics and Docking
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

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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BLASTOTool Content

http://oxytricha.princeton.edu/BlastO/index.html

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

BLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.

NAR Web Server Issue 2007
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tagsalgorithms animals automated pattern recognition computational biology genetic databases genome genomics humans nucleic acid sequence homology phylogeny species specificity

CIPResTool Content

http://www.phylo.org/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction

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

http://conseq.bioinfo.tau.ac.il/

Protein > 3-D Structural Features
Protein > Phylogeny Reconstruction
Protein > Sequence Features

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).

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tagsalgorithms amino acid sequence amino acid sequence homology amino acid substitution amino acids molecular sequence data protein sequence analysis proteins sequence alignment structure-activity relationship

cpnDBDatabase Content

http://www.cpndb.ca/cpnDB/home.php

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Protein > Sequence Data
Protein > Sequence Retrieval

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.

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tagsanimals bacteria base sequence chaperonin 60 computational biology genetic databases molecular sequence data nucleic acid sequence homology

CVTreeTool Content

http://tlife.fudan.edu.cn/cvtree

Model Organisms > Microbes
Protein > Phylogeny Reconstruction

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

NAR Web Server Issue 2004NAR Web Server Issue 2009
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tagsalgorithms archaeal genome bacteria bacterial genome chloroplast dna fungal genome genome genomics phylogeny viral genome viruses

d-OmixTool Content

http://www.biotec.or.th/isl/Domix

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

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.

NAR Web Server Issue 2009
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tagsphylogeny protein interaction domains and motifs proteins proteomics tertiary protein structure

FGFTool Content

http://fgf.genomics.org.cn/service/index.jsp

Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

FGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations).

NAR Web Server Issue 2007
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tagsalgorithms animals chromosome mapping chromosomes computational biology gene duplication genetic models genome humans molecular evolution phylogeny

iTOLTool Content

http://itol.embl.de

Protein > Phylogeny Reconstruction

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.

This content is being maintained by iletunic.

NAR Web Server Issue 2011
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tagsalgorithms animals chromosome mapping computational biology data display decision trees genetic databases humans molecular evolution phylogeny species specificity visualization

JEvTraceTool Content

http://www.cmpharm.ucsf.edu/~marcinj/JEvTrace/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

Jevtrace is a tool that combines multiple sequence alignments, phylogenetic, and structural data for identification of functional sites in proteins.

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tagsamino acid sequence amino acid sequence homology animals bacterial proteins binding sites carrier proteins conserved sequence dna-binding proteins factual databases genetic variation glucocorticoid receptors haemophilus influenzae humans molecular evolution molecular models molecular sequence data mutation phylogeny protein conformation proteins quaternary protein structure rats rna-binding proteins sequence alignment src homology domains streptococcus pneumoniae zinc fingers

Joes Site - Phylogeny ProgramsResource Content

http://evolution.genetics.washington.edu/phylip/software.html

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction

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

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MaxAlignTool Content

http://www.cbs.dtu.dk/services/MaxAlign/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Other Alignment Tools

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.

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tagsalgorithms automated pattern recognition genetic databases sequence alignment sequence analysis

MEGATool Content

http://www.megasoftware.net/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction

MEGA (Molecular Evolutionary Genetics Analysis) is a software package for phylogenetic analysis with a graphical user interface. It allows viewing and editing of the aligned input sequence data and provides many tools for phylogenetic and statistical analysis of the alignments.

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tagsdna dna sequence analysis genetic databases molecular evolution phylogeny protein sequence analysis proteins sequence alignment statistical data interpretation

MesquiteTool Content

http://mesquiteproject.org/mesquite/mesquite.html

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction

Mesquite is an open source software project designed to deal with comparative data about organisms and evolutionary analyses. Mesquite contains modules for phylogenetic analysis, population genetics, and non-phylogenetic multivariate analysis.

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Tags associated with subcategory 'Protein/Phylogeny Reconstruction'

phylogeny sequence alignment protein sequence analysis animals algorithms computational biology proteins molecular evolution humans genetic databases dna sequence analysis molecular sequence data amino acid sequence protein conformation amino acid sequence homology protein binding cytochrome p-450 enzyme system molecular models conserved sequence false positive reactions fungal proteins saccharomyces cerevisiae proteomics bayes theorem binding sites gene expression profiling artificial intelligence signal transduction chemical models succinate dehydrogenase drosophila proteins eukaryotic cells quaternary protein structure x-ray crystallography medicinal plants molecular cloning molecular structure lectins hydrogen bonding enzyme inhibitors fabaceae hiv integrase online systems ovomucin markov chains recombinant proteins systems integration protein structural homology protein interaction mapping plant lectins plant proteins proprotein convertases escherichia coli proteins src homology domains messenger rna protein databases genetic models genes dna evaluation studies as topic fibronectins protein-serine-threonine kinases reproducibility of results sequence analysis time factors computer simulation software validation nucleic acid sequence homology rna sequence analysis sensitivity and specificity factual databases consensus sequence base sequence color genomics chromosome mapping bacterial proteins statistical models tertiary protein structure bacterial genome open reading frames amino acid substitution database management systems likelihood functions mathematical computing information systems microcomputers amino acids structure-activity relationship statistical data interpretation chymotrypsin theoretical models ubiquitin gene expression human genome secondary protein structure probability bacterial genes chemical dictionaries initiator codon peptides