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Computational phylogenetics

Computational phylogenetics, phylogeny inference, or phylogenetic inference focuses on computational and optimization algorithms, heuristics, and approaches involved in phylogenetic analyses. The goal is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of genes, species, or taxa. Maximum likelihood, parsimony…

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Distance-matrix methods

Interior node UPGMA WPGMA Ultrametric Cluster analysis

21 related topics

Model selection

Molecular phylogenetics Transitions Transversions Coalescence Long branch attraction

19 related topics

Coding characters and defining homology

Matrix Convergent evolution Fossil Apes Data set

14 related topics

Types of phylogenetic trees and networks

Directed graph Most recent common ancestor Leaf nodes Genetic distance Molecular clock

9 related topics

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Overview

Algorithms Algorithm
Heuristics Heuristic (computer science)
Phylogenetic Phylogenetics
Phylogenetic tree
Genes Gene
Species
Taxa
Maximum likelihood Maximum likelihood estimation
Parsimony Maximum parsimony (phylogenetics)
Bayesian Bayesian inference in phylogeny
Minimum evolution
Tree rearrangements Tree rearrangement
Morphological Morphology (biology)
Phenotypic Phenotype
Nucleotide
Amino acid
Proteins Protein
Sequence alignment
Genomes Genome
Evolutionary tree
Polytomy
Bootstrap Bootstrapping (statistics)
Bayesian inference
Burn-in

Types of phylogenetic trees and networks

Directed graph
Most recent common ancestor
Leaf nodes Leaf node
Genetic distance
Molecular clock
Optimization Optimization (mathematics)
Phylogenetic networks Phylogenetic network
Hybridization Hybridisation (biology)
Horizontal gene transfer

Coding characters and defining homology

Matrix Matrix (mathematics)
Convergent evolution
Fossil
Apes Ape
Data set
DNA
RNA
Homology Homology (biology)
Multiple sequence alignments Multiple sequence alignment
Mutations Mutation
Insertion mutations Insertion (genetics)
Deletion mutations Deletion (genetics)
Orthologs Ortholog
Phylogenomics

Distance-matrix methods

Interior node
UPGMA
WPGMA
Ultrametric
Cluster analysis
Neighbor-joining
Fitch–Margoliash method Distance matrices in phylogeny
Least squares
Linear
Expected values Expected value
Substitution matrix
Jukes-Cantor model
Concentration of measure
Curse of dimensionality
NP-complete
Heuristic
Outgroup Outgroup (cladistics)
Experimental control
Noise Signal noise
Conserved Conservation (genetics)
Bacteria

Maximum parsimony

Maximum likelihood

Maximum likelihood
Probability distributions Probability distribution
Substitution model
Statistically independent
Dynamic programming
Global optimization
Newton–Raphson method

Bayesian inference

Model selection

Limitations and workarounds

The role of fossils

Living taxa Extant taxon
Stratocladistics

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Computational phylogenetics

Nodes126

Edges125

Triples9

Avg. degree1.98

Density0.015873

Components1

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Computational phylogenetics

Top relations

related to External links · 4

Computational phylogenetics → Computational, Media, Wikimedia Commons, Wiktionary-logo-en-v2

Important terminology Word statistics

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Important terminology

tree phylogenetic trees data methods method sequences evolutionary sequence used bayesian model phylogenetics likelihood may species maximum number related also

Entity relationships Subject–Predicate–Object triples

Subject	Predicate	Object	Confidence	Src
hybridization or horizontal gene transfer	instance of	which allow for the modeling of evolutionary phenomena	0.80	text
eyes or vertebrae	instance of	as is counting features	0.80	text
that derived from the Jukes-Cantor model of DNA evolution	instance of	This correction is done through the use of a substitution matrix	0.80	text
the Newton	instance of	general global optimization tools	0.80	text
speciation occur as stochastic processes	instance of	or may be a more sophisticated estimate derived from the assumption that divergence events	0.80	text
Computational phylogenetics	related to External links	Wiktionary-logo-en-v2	0.60	section
Computational phylogenetics	related to External links	Media	0.60	section
Computational phylogenetics	related to External links	Computational	0.60	section
Computational phylogenetics	related to External links	Wikimedia Commons	0.60	section

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