Large-Scale Multiple Sequence Alignment and Phylogeny Estimation
From MaRDI portal
Publication:4992756
DOI10.1007/978-1-4471-5298-9_6zbMath1462.92046OpenAlexW93958072MaRDI QIDQ4992756
Publication date: 10 June 2021
Published in: Models and Algorithms for Genome Evolution (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1007/978-1-4471-5298-9_6
incomplete lineage sortingedit distancehorizontal gene transfergeneral time reversibletrue alignment
Problems related to evolution (92D15) Protein sequences, DNA sequences (92D20) Research exposition (monographs, survey articles) pertaining to biology (92-02)
Related Items (4)
A measure of DNA sequence similarity by Fourier transform with applications on hierarchical clustering ⋮ An improved model for whole genome phylogenetic analysis by Fourier transform ⋮ Statistically consistent and computationally efficient inference of ancestral DNA sequences in the TKF91 model under dense taxon sampling ⋮ Detecting Locus Acquisition Events in Gene Trees
Uses Software
- MrBayes
- RAxML
- PAUP*
- BIONJ
- Balibase
- HMMER
- 3DCoffee
- ProbCons
- ClustalW
- BEAST
- LAGAN
- MUSCLE
- Kalign
- NAST
- Statalign
- Bali-phy
- Mugsy
- Infernal
- SABmark
- PartTree
- RIATA-HGT
- PROMALS
- OXBench
- ProtTest 3
- iGTP
- BUCKy
- Mauve
- SATe
- Probalign
- pplacer
- FastTree
- SuperFine
- TNT
- DACTAL
- Rec-I-DCM3
- Quartets MaxCut
- NINJA
- SATCHMO-JS
- SPEM
- MSACompro
- FASTSP
- COBALT
- GapCoder
- SEPP
- MLTreeMap
- POY
- Gegenees
Cites Work
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- Unnamed Item
- SATCHMO-JS
- SPEM
- MSACompro
- FASTSP
- COBALT
- GapCoder
- SEPP
- MLTreeMap
- POY
- Gegenees
- The performance of neighbor-joining methods of phylogenetic reconstruction
- Full reconstruction of Markov models on evolutionary trees: identifiability and consistency.
- Comparison of phylogenetic trees
- The Steiner problem in phylogeny is NP-complete
- Inverting random functions
- Recovering a tree from the leaf colourations it generates under a Markov model
- Links between maximum likelihood and maximum parsimony under a simple model of site substitution
- Phylogenetic supertrees. Combining information to reveal the tree of life
- New powerful statistics for alignment-free sequence comparison under a pattern transfer model
- Algorithm for statistical alignment of two sequences derived from a Poisson sequence length distribution
- Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters
- Approximation algorithms for tree alignment with a given phylogeny
- A few logs suffice to build (almost) all trees. II
- Identifying evolutionary trees and substitution parameters for the general Markov model with invariable sites
- Invertibility of the TKF model of sequence evolution
- A signal-to-noise analysis of phylogeny estimation by neighbor-joining: Insufficiency of polynomial length sequences
- Consistency of Bayesian inference of resolved phylogenetic trees
- Optimal phylogenetic reconstruction
- Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep
- Toward Extracting All Phylogenetic Information from Matrices of Evolutionary Distances
- Cache-oblivious dynamic programming
- Maximal Accurate Forests from Distance Matrices
- A measure of the similarity of sets of sequences not requiring sequence alignment.
- Minimal Mutation Trees of Sequences
- A few logs suffice to build (almost) all trees (I)
- Improved Approximation Algorithms for Tree Alignment
- A More Efficient Approximation Scheme for Tree Alignment
- From Gene Trees to Species Trees
- Inverting Random Functions II: Explicit Bounds for Discrete Maximum Likelihood Estimation, with Applications
- Identifiability of a Markovian model of molecular evolution with gamma-distributed rates
- Computing and Combinatorics
- Learning nonsingular phylogenies and hidden Markov models
This page was built for publication: Large-Scale Multiple Sequence Alignment and Phylogeny Estimation
