Phylogenetic & Molecular Genetics Terms and Definitions
analog -- A feature that appears similar in two taxa which have originated from two different ancestors. ancestor -- Any organism, population, or species from which some other organism, population, or species is descended by reproduction. apomorphy -- specialized (=derived) characters of an org...Tags: Phylogenetic, Molecular, Genetics, Terms, Definitions
2476 days ago
Tags: MimiLook, Phylogenetic, Workflow, Detection, Gene, Acquisition, Major, Orthologous, Groups, Megavirales
860 days ago
homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes
This tutorial describes the usage of homologizer to phase gene copies into polyploid subgenomes. The tutorial is an abbreviated version of a soon-to-be published paper in Methods in Molecular Biology. Please see that paper for many more details and practical considerations for running&n...Tags: homologizer, Phylogenetic, phasing, gene, copies, polyploid, subgenomes
351 days ago
Tags: RAMI, tool, identification, characterization, phylogenetic, clusters, microbial, communities
2477 days ago
Harvest: a suite of core-genome alignment and visualization tools
Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees. Tools Parsnp - Core-genome alignment and analysis Gingr - Interactive ...Tags: Harvest, alignment, visualization, intraspecific, microbial, genomes, recombination, detection, phylogenetic, trees
2354 days ago
Tags: kSNP3.0, SNP, detection, phylogenetic, analysis, genomes, alignment, reference, genome
2354 days ago
DendroPy: a Python library for phylogenetic computing
DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, ...Tags: DendroPy, Python, library, phylogenetic, computing
2218 days ago
MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times
MCMCTREE is a phylogenetic program for Bayesian estimation of species divergence times using soft fossil constraints under various molecular clock models. This is part of the PAML package. In this tutorial I will analyze an easy example modified from dataset of Inoue et al. (2...Tags: MCMCTREE, phylogenetic, program, Bayesian, estimation, species, divergence, times
2178 days ago