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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 46 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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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

CRISPRcomparTool Content

http://crispr.u-psud.fr/CRISPRcompar/

DNA > Phylogeny Reconstruction
Model Organisms > Microbes

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.

NAR Web Server Issue 2008
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tagsalleles bacteria bacterial typing techniques tandem repeat sequences

ITS2Tool Content

http://its2.bioapps.biozentrum.uni-wuerzburg.de/

DNA > Phylogeny Reconstruction
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

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.

NAR Web Server Issue 2006
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tagsanimals base sequence computational biology conserved sequence eukaryota fungal genome fungi genetic databases genetic markers genetic transcription invertebrates molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny plant genome plants ribosomal rna ribosomal spacer dna rna sequence analysis sequence alignment tertiary protein structure

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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MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

NAR Web Server Issue 2006
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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

MIRU-VNTRplusTool Content

http://www.miru-vntrplus.org

DNA > Phylogeny Reconstruction
Human Genome > Health and Disease
Model Organisms > Microbes

MIRU-VNTRplus allows users to analyze genotyping data of their Mycobacterium tuberculosis strains either alone or in comparison with the reference DB of strains. The web server also includes tools to search for similar strains, phylogenetic analysis and mapping of geographic information.

NAR Web Server Issue 2010
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tagsbacterial dna bacterial typing techniques cluster analysis dna fingerprinting genetic databases genetic polymorphism genotype humans interspersed repetitive sequences microbial sensitivity tests minisatellite repeats molecular epidemiology mycobacterium tuberculosis phylogeny restriction fragment length polymorphism tuberculosis

MLSTTool Content

http://www.mlst.net/

DNA > Phylogeny Reconstruction
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MLST (Multi Locus Sequence Typing) is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms using the sequences of internal fragments of seven house-keeping genes.

NAR Web Server Issue 2005
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tagsalleles bacteria bacterial dna bacterial genes bacterial meningitis bacterial typing techniques cerebrospinal fluid cluster analysis dna sequence analysis evaluation studies as topic gene frequency humans meningococcal infections molecular sequence data mycological typing techniques neisseria meningitidis nucleic acid databases pneumococcal meningitis polymerase chain reaction serotyping streptococcus pneumoniae virulence

ModelTest SeverTool Content

http://darwin.uvigo.es/software/modeltest_server.html

DNA > Phylogeny Reconstruction

ModelTest is program for the selection the model of DNA evolution (nucleotide substitution) that best fits your data from phylogenetic analyses.

NAR Web Server Issue 2006
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tagsalgorithms base composition bayes theorem biological models dna dna sequence analysis genetic variation likelihood functions molecular evolution nucleotides online systems sequence alignment statistical models

Tags associated with subcategory 'DNA/Phylogeny Reconstruction'

phylogeny sequence alignment dna sequence analysis animals computational biology algorithms humans protein sequence analysis molecular evolution genetic databases molecular sequence data proteins genomics base sequence chromosome mapping automated pattern recognition serotyping ascomycota streptococcus pneumoniae virulence complementary dna classification gene library hordeum host-parasite interactions expressed sequence tags exons cluster analysis codon polymerase chain reaction disease susceptibility mycological typing techniques pneumococcal meningitis protozoan dna protozoan genes rats plasmodium vivax plasmodium falciparum conserved sequence gene components mice software design untranslated rna meningococcal infections nucleic acid databases neisseria meningitidis gene frequency cerebrospinal fluid systems integration bacterial genes bacterial meningitis bacterial typing techniques species specificity peptides genetic models messenger rna protein conformation genes fibronectins consensus sequence dna evaluation studies as topic protein databases protein-serine-threonine kinases sequence analysis time factors computer simulation software validation nucleic acid sequence homology reproducibility of results rna sequence analysis sensitivity and specificity factual databases mathematical computing likelihood functions symbiosis amino acid sequence homology artificial intelligence theoretical models reading frames plant dna plant genome plants bayes theorem binding sites microcomputers information systems database management systems statistical data interpretation tertiary protein structure gene expression profiling markov chains src homology domains statistical models viral genome takifugu sequence tagged sites united states archaea phenotype neoplasms