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Glutton: large-scale integration of non-model organism transcriptome data for comparative analysis

https://doi.org/10.1101/077511
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What this work says

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

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Full-length transcriptome assembly from RNA-Seq data without a reference genome
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The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera
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De novo assembly and analysis of RNA-seq data
inferredcites →https://doi.org/10.1038/nrg2484openalex-snapshot
RNA-Seq: a revolutionary tool for transcriptomics
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A collection of Australian Drosophila datasets on climate adaptation and species distributions
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An algorithm for progressive multiple alignment of sequences with insertions
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Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life
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Beta Regression for Modelling Rates and Proportions
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Oases:robustde novoRNA-seq assembly across the dynamic range of expression levels
inferredcites →https://doi.org/10.1093/bioinformatics/bts198openalex-snapshot
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm
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/btu077openalex-snapshot
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
inferredcites →https://doi.org/10.1093/bioinformatics/btu613openalex-snapshot
The Ensembl REST API: Ensembl Data for Any Language
inferredcites →https://doi.org/10.1093/database/bar030openalex-snapshot
Ensembl BioMarts: a hub for data retrieval across taxonomic space
inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msq115openalex-snapshot
The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection
inferredcites →https://doi.org/10.1093/molbev/msr177openalex-snapshot
Improving the Performance of Positive Selection Inference by Filtering Unreliable Alignment Regions
inferredcites →https://doi.org/10.1093/molbev/msr272openalex-snapshot
The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection
inferredcites →https://doi.org/10.1093/molbev/msv037openalex-snapshot
Tree of Life Reveals Clock-Like Speciation and Diversification
inferredcites →https://doi.org/10.1093/molbev/msv333openalex-snapshot
Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization
inferredcites →https://doi.org/10.1093/nar/gkr854openalex-snapshot
The sequence read archive: explosive growth of sequencing data
inferredcites →https://doi.org/10.1093/nar/gkv1209openalex-snapshot
Ensembl Genomes 2016: more genomes, more complexity
inferredcites →https://doi.org/10.1093/sysbio/syu011openalex-snapshot
Competitive Release Leads to Range Expansion and Rampant Speciation in Malagasy Dung Beetles
inferredcites →https://doi.org/10.1101/gr.073585.107openalex-snapshot
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
inferredcites →https://doi.org/10.1101/gr.103846.109openalex-snapshot
Optimization of de novo transcriptome assembly from next-generation sequencing data
inferredcites →https://doi.org/10.1111/1755-0998.12465openalex-snapshot
Optimization of next‐generation sequencing transcriptome annotation for species lacking sequenced genomes
inferredcites →https://doi.org/10.1111/syen.12063openalex-snapshot
Evolution of the M alagasy endemic genus Nanos W estwood, 1842 ( C oleoptera, S carabaeidae, E pilissini)
inferredcites →https://doi.org/10.1126/science.1158395openalex-snapshot
Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
inferredcites →https://doi.org/10.1126/science.1257570openalex-snapshot
Phylogenomics resolves the timing and pattern of insect evolution
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/2047-217x-3-1openalex-snapshot
CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy
inferredcites →https://doi.org/10.1186/2047-217x-3-17openalex-snapshot
Data access for the 1,000 Plants (1KP) project
inferredcites →https://doi.org/10.1186/s12862-014-0235-7openalex-snapshot
Séance: reference-based phylogenetic analysis for 18S rRNA studies
inferredcites →https://doi.org/10.1534/genetics.104.032144openalex-snapshot
Detecting Amino Acid Sites Under Positive Selection and Purifying Selection
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.3390/insects2020112openalex-snapshot
Origin and Diversification of Dung Beetles in Madagascar
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

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

inferred← citeshttps://doi.org/10.1534/g3.119.400357openalex-snapshot
Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris
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