PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
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Summary
PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick‐start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another.
- Type
- article
- Published
- 2019-11-06
- Cited by
- 3,469
- References
- 31
- Access
- Open access
- OpenAlex
- https://openalex.org/W2979811825
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:92664741
Keywords
Biology, Phylogenetics, Scalability, Sequence (biology), Evolutionary biology
References
- FeatureExtract—extraction of sequence annotation made easy
- Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system
- Parallel Implementation of MAFFT on CUDA-Enabled Graphics Hardware
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- A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives
- EPoS: a modular software framework for phylogenetic analysis
- Buying in to bioinformatics: an introduction to commercial sequence analysis software
- IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
- trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
- Recent trends in molecular phylogenetic analysis: where to next?
- Sequencing technologies — the next generation
- Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
- SequenceMatrix: concatenation software for the fast assembly of multi‐gene datasets with character set and codon information
- Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.
- MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
- Gene tree discordance, phylogenetic inference and the multispecies coalescent.
- Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
- Armadillo 1.1: An Original Workflow Platform for Designing and Conducting Phylogenetic Analysis and Simulations
- LS³: A Method for Improving Phylogenomic Inferences When Evolutionary Rates Are Heterogeneous among Taxa
Cited by
- Characterization of the complete mitochondrial genome of Nippotaenia mogurndae Yamaguti and Miyata, 1940 (Cestoda: Nippotaeniidae).
- The mitochondrial genomes of three skippers: Insights into the evolution of the family Hesperiidae (Lepidoptera).
- Characterization of the complete mitochondrial genome of Plagiorchis maculosus (Digenea, Plagiorchiidae), Representative of a taxonomically complex digenean family.
- Molecular characterization of a new potyvirus infecting passion fruit
- Characterization of the complete mitochondrial genome of Uvitellina sp., representative of the family Cyclocoelidae and phylogenetic implications
- Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda
- Plastome phylogenomics of Saussurea (Asteraceae: Cardueae)
- Characterization and phylogenomics of the complete mitochondrial genome of the polyzoic cestode Gangesia oligonchis (Platyhelminthes: Onchoproteocephalidea).
- The complete mitochondrial genome of Cryptotermes declivis Tsai et Chen (Isoptera: Kalotermitidae)
- The complete mitochondrial genome of West Indian drywood termite, Cryptotermes brevis (Walker) (Isoptera: Kalotermitidae)
- Complete plastid genome of Gentiana trichotoma (Gentianaceae) and phylogenetic analysis
- Structural features and phylogenetic implications of four new mitogenomes of Centrotinae (Hemiptera: Membracidae).
- Complete mitochondrial genomes of Bittacus strigosus and Panorpa debilis and genomic comparisons of Mecoptera.
- The complete mitochondrial genome of Pyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world’s largest frogs
- Phylogenetic relationships and phylogeography of the genus Sinocyrtaspis Liu, 2000 (Orthoptera: Tettigoniidae: Meconematinae) reveal speciation processes related to climate change
- Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics
- Mitochondrial Genomes of Two Thaparocleidus Species (Platyhelminthes: Monogenea) Reveal the First rRNA Gene Rearrangement among the Neodermata
- Characterization of the complete mitochondrial genomes of two species of the genus Aphaena Guérin-Méneville (Hemiptera: Fulgoridae) and its phylogenetic implications.
- The complete mitochondrial genome of the largest amphipod, Alicella gigantea: Insight into its phylogenetic relationships and deep sea adaptive characters.
- Phylogeny, origin and dispersal of Saussurea (Asteraceae) based on chloroplast genome data.
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