Computational phylogenetics | Wikipedia audio article
Channel: wikipedia tts
Date: 2019-01-13

This is an audio version of the Wikipedia Article:
https://en.wikipedia.org/wiki/Computational_phylogenetics


00:01:49 1 Types of phylogenetic trees and networks
00:04:15 2 Coding characters and defining homology
00:04:27 2.1 Morphological analysis
00:08:02 2.2 Molecular analysis
00:09:35 3 Distance-matrix methods
00:11:08 3.1 UPGMA and WPGMA
00:11:43 3.2 Neighbor-joining
00:12:15 3.3 Fitch-Margoliash method
00:14:48 3.4 Using outgroups
00:16:22 4 Maximum parsimony
00:18:04 4.1 Branch and bound
00:20:04 4.2 Sankoff-Morel-Cedergren algorithm
00:21:34 4.3 MALIGN and POY
00:22:43 5 Maximum likelihood
00:25:01 6 Bayesian inference
00:27:21 7 Model selection
00:29:09 7.1 Types of models
00:31:59 7.2 Choosing the best model
00:35:16 8 Evaluating tree support
00:35:59 8.1 Nodal support
00:36:32 8.1.1 Consensus tree
00:37:48 8.1.2 Bootstrapping and jackknifing
00:40:32 8.1.3 Posterior probability
00:41:57 8.1.4 Step counting methods
00:42:13 8.2 Shortcomings
00:42:47 9 Limitations and workarounds
00:43:32 9.1 Homoplasy
00:45:08 9.2 Horizontal gene transfer
00:46:43 9.3 Hybrids, speciation, introgressions and incomplete  lineage sorting
00:48:22 9.4 Taxon sampling
00:49:25 9.5 Phylogenetic signal
00:50:01 9.6 Continuous characters
00:51:32 9.7 Missing data
00:52:11 10 The role of fossils
00:53:22 11 See also



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SUMMARY
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Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa. For example, these techniques have been used to explore the family tree of hominid species and the relationships between specific genes shared by many types of organisms. Traditional phylogenetics relies on morphological data obtained by measuring and quantifying the phenotypic properties of representative organisms, while the more recent field of molecular phylogenetics uses nucleotide sequences encoding genes or amino acid sequences encoding proteins as the basis for classification. Many forms of molecular phylogenetics are closely related to and make extensive use of sequence alignment in constructing and refining phylogenetic trees, which are used to classify the evolutionary relationships between homologous genes represented in the genomes of divergent species. The phylogenetic trees constructed by computational methods are unlikely to perfectly reproduce the evolutionary tree that represents the historical relationships between the species being analyzed. The historical species tree may also differ from the historical tree of an individual homologous gene shared by those species.