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DiscoMark: Nuclear marker discovery from orthologous sequences using draft genome data

https://doi.org/10.1101/047282
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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One hundred new universal exonic markers for birds developed from a genomic pipeline
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Genome sequencing and population genomics in non-model organisms
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Endemism and diversification in freshwater insects of Madagascar revealed by coalescent and phylogenetic analysis of museum and field collections
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A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach
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Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times
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jModelTest 2: more models, new heuristics and parallel computing
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Resolution of ray-finned fish phylogeny and timing of diversification
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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
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Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments
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A New Statistical Method for Haplotype Reconstruction from Population Data
inferredcites →https://doi.org/10.1086/379378openalex-snapshot
A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype Data
inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu832openalex-snapshot
PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btv069openalex-snapshot
PolyMarker: A fast polyploid primer design pipeline
inferredcites →https://doi.org/10.1093/bioinformatics/btv420openalex-snapshot
CEMAsuite: open source degenerate PCR primer design
inferredcites →https://doi.org/10.1093/bioinformatics/btv717openalex-snapshot
Fitchi: haplotype genealogy graphs based on the Fitch algorithm
inferredcites →https://doi.org/10.1093/molbev/msm060openalex-snapshot
Heads or Tails: A Simple Reliability Check for Multiple Sequence Alignments
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/gki425openalex-snapshot
PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs
inferredcites →https://doi.org/10.1093/nar/gks596openalex-snapshot
Primer3—new capabilities and interfaces
inferredcites →https://doi.org/10.1093/nar/gkv318openalex-snapshot
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026334openalex-snapshot
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
inferredcites →https://doi.org/10.1093/sysbio/sys004openalex-snapshot
Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
inferredcites →https://doi.org/10.1093/sysbio/sys029openalex-snapshot
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
inferredcites →https://doi.org/10.1093/sysbio/sys051openalex-snapshot
High-Throughput Identification of Informative Nuclear Loci for Shallow-Scale Phylogenetics and Phylogeography
inferredcites →https://doi.org/10.1093/sysbio/syt099openalex-snapshot
Coalescent Species Delimitation in Milksnakes (Genus Lampropeltis) and Impacts on Phylogenetic Comparative Analyses
inferredcites →https://doi.org/10.1111/1755-0998.12403openalex-snapshot
Scrimer: designing primers from transcriptome data
inferredcites →https://doi.org/10.1111/fwb.12450openalex-snapshot
Evolution and island endemism of morphologically cryptic Baetis and Cloeon species (Ephemeroptera, Baetidae) on the Canary Islands and Madeira
inferredcites →https://doi.org/10.1111/j.1755-0998.2008.02241.xopenalex-snapshot
Computation vs. cloning: evaluation of two methods for haplotype determination
inferredcites →https://doi.org/10.1111/j.1755-0998.2009.02732.xopenalex-snapshot
seqphase : a web tool for interconverting phase input/output files and fasta sequence alignments
inferredcites →https://doi.org/10.1146/annurev-ento-011613-161958openalex-snapshot
Freshwater Biodiversity and Aquatic Insect Diversification
inferredcites →https://doi.org/10.1155/2012/783138openalex-snapshot
Gemi: PCR Primers Prediction from Multiple Alignments
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-14-255openalex-snapshot
A multiple-alignment based primer design algorithm for genetically highly variable DNA targets
inferredcites →https://doi.org/10.1186/1471-2105-9-253openalex-snapshot
BatchPrimer3: A high throughput web application for PCR and sequencing primer design
inferredcites →https://doi.org/10.1186/1471-2148-10-118openalex-snapshot
Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation
inferredcites →https://doi.org/10.1186/1471-2148-12-26openalex-snapshot
Cryptic variation in an ecological indicator organism: mitochondrial and nuclear DNA sequence data confirm distinct lineages of Baetis harrisoni Barnard (Ephemeroptera: Baetidae) in southern Africa
inferredcites →https://doi.org/10.1186/1471-2148-9-157openalex-snapshot
HaMStR: Profile hidden markov model based search for orthologs in ESTs
inferredcites →https://doi.org/10.1186/1748-7188-9-4openalex-snapshot
Assessing the efficiency of multiple sequence alignment programs
inferredcites →https://doi.org/10.1186/s12862-016-0643-yopenalex-snapshot
Distribution and population genetic variation of cryptic species of the Alpine mayfly Baetis alpinus (Ephemeroptera: Baetidae) in the Central Alps
inferredcites →https://doi.org/10.1186/s13029-015-0038-2openalex-snapshot
PrimerView: high-throughput primer design and visualization
inferredcites →https://doi.org/10.1364/oe.23.031640openalex-snapshot
Two-dimensional polymer grating and prism on Bloch surface waves platform
inferredcites →https://doi.org/10.1371/journal.pcbi.1004447openalex-snapshot
ReproPhylo: An Environment for Reproducible Phylogenomics
inferredcites →https://doi.org/10.1371/journal.pone.0003376openalex-snapshot
Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
inferredcites →https://doi.org/10.1371/journal.pone.0019379openalex-snapshot
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
inferredcites →https://doi.org/10.1371/journal.pone.0019728openalex-snapshot
Toward a DNA Taxonomy of Alpine Rhithrogena (Ephemeroptera: Heptageniidae) Using a Mixed Yule-Coalescent Analysis of Mitochondrial and Nuclear DNA
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MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s13225-020-00455-5openalex-snapshot
Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics
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