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Links tagged with 'likelihood functions'

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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

McPromoterTool Content

http://genes.mit.edu/McPromoter.html

DNA > Structure and Sequence Feature Detection

The Markov Chain Promoter Prediction Server (McPromoter) uses statistics to predict eukaryotic DNA transcription start sites.

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tagsanimals computational biology dna drosophila genetic models genetic promoter regions likelihood functions markov chains neural networks (computer) nucleic acid databases physical chemistry physicochemical phenomena statistical models stochastic processes

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

MultiPhylTool Content

http://www.cs.nuim.ie/distributed/multiphyl.php

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

MultiPhyl is a high-throughput Maximum Likelihood based phylogeny analysis program that allows researchers to create a virtual phylogenetic supercomputer from a group semi-idle desktop machines.

NAR Web Server Issue 2007
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tagsalgorithms animals computational biology computer simulation computing methodologies dna sequence analysis genetic databases genetic models genomics humans likelihood functions molecular evolution phylogeny sequence alignment statistical models

TREE-PUZZLETool Content

http://www.tree-puzzle.de/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction

Tree-puzzle is a program that constructs phylogenetic trees from sequence alignments using the maximum likelihood method.

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tagsalgorithms computing methodologies database management systems genetic databases likelihood functions mathematical computing molecular sequence data phylogeny sequence analysis

WebFEATURETool Content

http://feature.stanford.edu/webfeature/

Protein > 3-D Structural Features
Protein > Domains and Motifs
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.

NAR Web Server Issue 2003
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tagsalgorithms bayes theorem binding sites calcium calcium-binding proteins computational biology factual databases genomics likelihood functions macromolecular substances molecular models molecular structure nucleic acid conformation nucleic acids protein conformation proteins reproducibility of results sensitivity and specificity statistical models