PAML 4: phylogenetic analysis by maximum likelihood.

By Ziheng Yang. Molecular biology and evolution, 2007

12,910 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/da7ab2f1b6278472f3671a7430c9a72bad07781f

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. Sudhir Kumar
2. Koichiro Tamura
3. Ziheng Yang
4. Guangchuang Yu
5. Masatoshi Nei
6. Remco R. Bouckaert
7. Glen Stecher
8. Ari Löytynoja

In Molecular Biology

1. Sudhir Kumar
2. Koichiro Tamura
3. Guangchuang Yu
4. Masatoshi Nei
5. Zhang Zhang
6. Ziheng Yang
7. Glen Stecher
8. Jaime Huerta-Cepas

In Paleontology

1. Guangchuang Yu
2. Koichiro Tamura
3. Sudhir Kumar
4. Remco R. Bouckaert
5. Alexei J. Drummond
6. James F. Parham
7. W. Joyce
8. Zehan Dai

Citations in the corpus

• Molecular phylogeny and evolution of the Asian lineage of vole genus Microtus (Rodentia: Arvicolinae) inferred from mitochondrial cytochrome b sequence (2010, methodology): “Rate heterogeneity among taxa was determined with the use of hierarchical likelihood ratio tests as implemented in PAML, version 4.0 (Yang, 2007) and relative-rate tests as implemented in RRTree (Robinson et al., 1998; Robinson-Rechavi & Huchon, 2000).”
• webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser (2010, methodology): “Yang Z: PAML 4: Phylogenetic analysis by maximum likelihood.”
• Molecular phylogeny and evolution of the Perissodactyla (2011, methodology): “…the Bayesian relaxed molecular clock approach, was used to estimate divergence times by calculating branch lengths and the variance-covariance matrix from the mitochondrial and nuclear datasets using the Felsenstein (F84) + G model, with ML parameters obtained from PAML 4 v. 3.1 (Yang, 2007).”
• The Population Genetics of dN/dS (2008, methodology): “Theoretical work on the relationship between dN/dS and selection likewise assumes that sequences are sampled from independent, divergent species [3],as do computer packages used to estimate dN/dS from data [6, 7 ].”
• The Amborella Genome and the Evolution of Flowering Plants (2013, background): “Salzberg, TopHat: discovering splice junctions with RNASeq, Bioinformatics 25, 1105–1111 (2009).”
• WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes (2021, methodology): “Non-synonymous (Ka) and synonymous (Ks) substitution rates are estimated using the Nei-Gojobori method implemented in the YN00 program in the PAML (4.9h)(Yang 2007) package.”
• Phylogenetic relationships of Santalales with insights into the origins of holoparasitic Balanophoraceae (2015, methodology): “Each of the seven resulting trimmed trees was loaded into PAML v.4.3 (Yang, 2007) along with the corresponding individual gene dataset, and branch lengths of the trimmed tree and substitution model parameters were estimated for each gene.”