Compared with ML method, is NJ method more suitable for SNP information to construct phylogenetic trees?
Best insight from top research papers
The neighbor joining (NJ) method is generally more suitable than the maximum likelihood (ML) method for constructing phylogenetic trees based on SNP information . Computer simulations have shown that the NJ method with p distance (NJp method) gives better performance than other methods, regardless of whether the gene is compositional or contains mosaic DNA regions . NJp method generally gives a high value of the combined quantity (c), which indicates a good data-fit model . Additionally, the SNPhylo pipeline, which uses a maximum likelihood method, is specifically designed to construct phylogenetic trees based on large SNP datasets . Therefore, the NJ method is more accurate and suitable for constructing phylogenetic trees using SNP information compared to the ML method.
Answers from top 5 papers
More filters
| Papers (5) | Insight |
|---|---|
| The provided paper does not compare the Neighbor Joining (NJ) method with the Maximum Likelihood (ML) method for constructing phylogenetic trees using SNP information. | |
| The paper does not compare the suitability of the NJ method and the ML method for constructing phylogenetic trees using SNP information. | |
34 Citations | The paper does not directly compare the suitability of the NJ method and the ML method for SNP information in constructing phylogenetic trees. |
| The paper does not mention whether the NJ method is more suitable than the ML method for constructing phylogenetic trees using SNP information. | |
| The paper does not directly compare the suitability of the NJ and ML methods for SNP information in constructing phylogenetic trees. |
Related Questions
What is a phylogeographic tree?4 answersA phylogeographic tree is an evolutionary reconstruction that depicts the geographic spread and genetic relationships of taxa or gene lineages. These trees are crucial in studying the origin, diversification, and spread of species, especially in the context of pathogen outbreaks, speciation, and population ecology. By overlaying geographical information onto gene trees, researchers can analyze the associations between genetic variation, spatial distribution, and evolutionary history, providing insights into historical events like range expansions, fragmentation, and gene flow. Phylogeographic trees are constructed using genetic sequences, such as mitochondrial or nuclear DNA markers, and are instrumental in understanding post-glacial recolonization, identifying suture zones, and estimating the impact of historical events like the Last Glacial Maximum on mammal populations in Europe.
What is assumed when creating SNP trees with CSI phylogeny?5 answersWhen creating SNP trees with CSI phylogeny, it is assumed that the method involves inferring species trees by minimizing deep coalescences under an infinite sites model, which is equivalent to the concept of polymorphism parsimony. This approach requires thinning of data sets to statistically independent sites and allows for the estimation of a rooted tree, enhancing scalability and accuracy in large-scale phylogenomic data sets. Additionally, the use of SNP data in constructing phylogenetic trees necessitates steps to ensure reliability, such as removing low-quality data and considering linkage disequilibrium. Integrating metadata along with SNP data in the analysis process can provide valuable insights into the evolutionary history and phenotypic characteristics of the samples, enhancing the overall understanding of the phylogenetic relationships.
How to construct phylogeny trees with DNA sequences using MEGA?4 answersBuilding phylogeny trees with DNA sequences using MEGA involves several steps. First, data needs to be collected from GenBank and inserted into a text editor. Then, the data can be imported into MEGA, which is a user-friendly software for building evolutionary trees. MEGA offers different methods for constructing phylogenetic trees, such as neighbor joining and maximum likelihood. The software also provides options for aligning the sequences using algorithms like ClustalW and MUSCLE. Additionally, MEGA allows users to select the most suitable substitution model for the maximum likelihood method. Finally, MEGA provides a flexible interface for drawing the final tree for publication. By following these steps, users can construct phylogeny trees using DNA sequences in MEGA.
What are the advantages and disadvantages of using SNIPs (Single Nucleotide Polymorphisms) in phylogenetic studies?4 answersSingle Nucleotide Polymorphisms (SNPs) have advantages and disadvantages in phylogenetic studies. SNPs are widely used molecular markers that can help understand the relationship between phenotypes and genotypes. They provide valuable information about the genetic basis of common diseases, complex traits, and the origins and ancestry of human populations. In phylogenetic studies, SNPs offer scalability and the ability to estimate rooted trees. However, there are also challenges associated with using SNPs. One challenge is the low agreement among different software in predicting SNPs, which can affect consistency and accuracy. Another challenge is the need to filter and impute missing values in SNP datasets to avoid misinterpretation and distortion in visual representations. Despite these challenges, SNPs are valuable markers that can increase the number of markers used in molecular evolution studies, enhancing our understanding of the tree of life.
Can snp genotypes be derived from non-model species?5 answersSNP genotypes can be derived from non-model species using various methods such as Genotyping-by-Sequencing (GBS) and SNP arrays. GBS was used to discover SNP markers for population structure and genomic diversity in the hazel dormouse Muscardinus avellanarius. The cross-species application of the Affymetrix 600K Chicken SNP array was successful in five species of North American prairie grouse, demonstrating the feasibility of using commercial SNP arrays in non-model bird species. DArTseq derived SNP data was used to identify genes linked to SNP associated sequence tags in the Australian native freshwater fish Macquaria ambigua, providing insight into genome evolution. SNP ascertainment can also be performed directly from published genome contigs and short-read archive data, enabling population genotyping in non-model organisms. In Eucalyptus cladocalyx, a high-density SNP array developed for commercial Eucalyptus was used to genotype a breeding population, highlighting the usefulness of SNP arrays for species with limited representation.
What software uses phylogenetic analysis?7 answers