Search Results - "Molecular ecology resources"

PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies by Zhang, Dong, Gao, Fangluan, Jakovlić, Ivan, Zou, Hong, Zhang, Jin, Li, Wen X., Wang, Gui T.

“…Multigene and genomic data sets have become commonplace in the field of phylogenetics, but many existing tools are not designed for such data sets, which often…”
Get full text

ASAP: assemble species by automatic partitioning by Puillandre, Nicolas, Brouillet, Sophie, Achaz, Guillaume

“…Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e.,…”
Get full text

CPGView: A package for visualizing detailed chloroplast genome structures by Liu, Shengyu, Ni, Yang, Li, Jingling, Zhang, Xinyi, Yang, Heyu, Chen, Haimei, Liu, Chang

“…Chloroplast genomes have been widely used in studying plant phylogeny and evolution. Several chloroplast genome visualization tools have been developed to…”
Get full text

Dsuite ‐ Fast D‐statistics and related admixture evidence from VCF files by Malinsky, Milan, Matschiner, Michael, Svardal, Hannes

“…Patterson's D, also known as the ABBA‐BABA statistic, and related statistics such as the f4‐ratio, are commonly used to assess evidence of gene flow between…”
Get full text

MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics by Allio, Rémi, Schomaker‐Bastos, Alex, Romiguier, Jonathan, Prosdocimi, Francisco, Nabholz, Benoit, Delsuc, Frédéric

“…Thanks to the development of high‐throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows…”
Get full text

dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing by Gruber, Bernd, Unmack, Peter J., Berry, Oliver F., Georges, Arthur

“…Although vast technological advances have been made and genetic software packages are growing in number, it is not a trivial task to analyse SNP data. We…”
Get full text

Clumpak: a program for identifying clustering modes and packaging population structure inferences across K by Kopelman, Naama M., Mayzel, Jonathan, Jakobsson, Mattias, Rosenberg, Noah A., Mayrose, Itay

“…The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population‐genetic data…”
Get full text

pophelper: an R package and web app to analyse and visualize population structure by Francis, R. M.

“…The pophelper r package and web app are software tools to aid in population structure analyses. They can be used for the analyses and visualization of output…”
Get full text

StructureSelector: A web‐based software to select and visualize the optimal number of clusters using multiple methods by Li, Yu‐Long, Liu, Jin‐Xian

“…Inferences of population genetic structure are of great importance to the fields of ecology and evolutionary biology. The program structure has been widely…”
Get full text

pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data by Korunes, Katharine L., Samuk, Kieran

“…Population genetic analyses often use summary statistics to describe patterns of genetic variation and provide insight into evolutionary processes. Among the…”
Get full text

genodive version 3.0: Easy‐to‐use software for the analysis of genetic data of diploids and polyploids by Meirmans, Patrick G.

“…genodive version 3.0 is a user‐friendly program for the analysis of population genetic data. This version presents a major update from the previous version and…”
Get full text

vcfr: a package to manipulate and visualize variant call format data in R by Knaus, Brian J., Grünwald, Niklaus J.

“…Software to call single‐nucleotide polymorphisms or related genetic variants has converged on the variant call format (VCF) as the output format of choice…”
Get full text

pcadapt: an R package to perform genome scans for selection based on principal component analysis by Luu, Keurcien, Bazin, Eric, Blum, Michael G. B.

“…The R package pcadapt performs genome scans to detect genes under selection based on population genomic data. It assumes that candidate markers are outliers…”
Get full text

program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem by Puechmaille, Sebastien J.

“…Inferences of population structure and more precisely the identification of genetically homogeneous groups of individuals are essential to the fields of…”
Get full text

obitools: a unix‐inspired software package for DNA metabarcoding by Boyer, Frédéric, Mercier, Céline, Bonin, Aurélie, Le Bras, Yvan, Taberlet, Pierre, Coissac, Eric

“…DNA metabarcoding offers new perspectives in biodiversity research. This recently developed approach to ecosystem study relies heavily on the use of…”
Get full text

Minor allele frequency thresholds strongly affect population structure inference with genomic data sets by Linck, Ethan, Battey, C. J.

“…A common method of minimizing errors in large DNA sequence data sets is to drop variable sites with a minor allele frequency (MAF) below some specified…”
Get full text

NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data by Do, C., Waples, R. S., Peel, D., Macbeth, G. M., Tillett, B. J., Ovenden, J. R.

“…NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several…”
Get full text

SymPortal: A novel analytical framework and platform for coral algal symbiont next‐generation sequencing ITS2 profiling by Hume, Benjamin C. C., Smith, Edward G., Ziegler, Maren, Warrington, Hugh J. M., Burt, John A., LaJeunesse, Todd C., Wiedenmann, Joerg, Voolstra, Christian R.

“…We present SymPortal (SymPortal.org), a novel analytical framework and platform for genetically resolving the algal symbionts of reef corals using…”
Get full text

Genetic structure and insecticide resistance characteristics of fall armyworm populations invading China by Zhang, Lei, Liu, Bo, Zheng, Weigang, Liu, Conghui, Zhang, Dandan, Zhao, Shengyuan, Li, Zaiyuan, Xu, Pengjun, Wilson, Kenneth, Withers, Amy, Jones, Christopher M., Smith, Judith A., Chipabika, Gilson, Kachigamba, Donald L., Nam, Kiwoong, d’Alençon, Emmanuelle, Liu, Bei, Liang, Xinyue, Jin, Minghui, Wu, Chao, Chakrabarty, Swapan, Yang, Xianming, Jiang, Yuying, Liu, Jie, Liu, Xiaolin, Quan, Weipeng, Wang, Guirong, Fan, Wei, Qian, Wanqiang, Wu, Kongming, Xiao, Yutao

“…The rapid wide‐scale spread of fall armyworm (Spodoptera frugiperda) has caused serious crop losses globally. However, differences in the genetic background of…”
Get full text

Breaking RAD: an evaluation of the utility of restriction site‐associated DNA sequencing for genome scans of adaptation by Lowry, David B., Hoban, Sean, Kelley, Joanna L., Lotterhos, Katie E., Reed, Laura K., Antolin, Michael F., Storfer, Andrew

“…Understanding how and why populations evolve is of fundamental importance to molecular ecology. Restriction site‐associated DNA sequencing (RADseq), a popular…”
Get full text