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Co-estimation of Phylogeny-aware Alignment and Phylogenetic Tree

https://doi.org/10.1101/077503
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What this work says

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

inferredcites →https://doi.org/10.1007/978-1-62703-646-7_10openalex-snapshot
Phylogeny-aware alignment with PRANK
inferredcites →https://doi.org/10.1007/bf02257378openalex-snapshot
The alignment of sets of sequences and the construction of phyletic trees: An integrated method
inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot
Comparison of phylogenetic trees
inferredcites →https://doi.org/10.1073/pnas.0409137102openalex-snapshot
An algorithm for progressive multiple alignment of sequences with insertions
inferredcites →https://doi.org/10.1073/pnas.1405628111openalex-snapshot
Simple chained guide trees give high-quality protein multiple sequence alignments
inferredcites →https://doi.org/10.1073/pnas.1417526112openalex-snapshot
Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks
inferredcites →https://doi.org/10.1080/10635150290102339openalex-snapshot
Increased Taxon Sampling Greatly Reduces Phylogenetic Error
inferredcites →https://doi.org/10.1093/bioinformatics/btm404openalex-snapshot
Clustal W and Clustal X version 2.0
inferredcites →https://doi.org/10.1093/bioinformatics/btq228openalex-snapshot
DendroPy: a Python library for phylogenetic computing
inferredcites →https://doi.org/10.1093/bioinformatics/btr701openalex-snapshot
Measuring the distance between multiple sequence alignments
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/molbev/msp098openalex-snapshot
INDELible: A Flexible Simulator of Biological Sequence Evolution
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/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040454openalex-snapshot
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
inferredcites →https://doi.org/10.1093/sysbio/syr095openalex-snapshot
SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees
inferredcites →https://doi.org/10.1101/gr.115949.110openalex-snapshot
High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes
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.1171243openalex-snapshot
Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees
inferredcites →https://doi.org/10.1126/science.1175949openalex-snapshot
Uniting Alignments and Trees

What points at this work

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

inferred← citeshttps://doi.org/10.1007/978-1-0716-1036-7_2openalex-snapshot
Phylogeny-Aware Alignment with PRANK and PAGAN
inferred← citeshttps://doi.org/10.1016/b978-0-443-21903-0.00006-0openalex-snapshot
How to conduct phylogenetic analysis with molecular data
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