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PAML specifications


Unique identifier OMICS_04238
Alternative name Phylogenetic Analysis by Maximum Likelihood
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
Computer skills Advanced
Version 4.0
Stability Stable
Maintained Yes


  • codeml
  • MCMCTree




No version available



  • person_outline Ziheng Yang

Publications for Phylogenetic Analysis by Maximum Likelihood

PAML citations


Chitinase genes (CHIAs) provide genomic footprints of a post Cretaceous dietary radiation in placental mammals

Sci Adv
PMCID: 5955627
PMID: 29774238
DOI: 10.1126/sciadv.aar6478

[…] g analyses, with shared inactivating mutations (table S4) providing a minimum branch on which pseudogenization occurred. We performed separate analyses for each CHIA paralog (data set S1) using PAML (phylogenetic analysis by maximum likelihood) v. 4.8 (), implementing two separate codon model assumptions (F1X4 and F3X4) and assuming the topology and divergence times of Emerling et al. (). We remov […]


Amino acid compositions contribute to the proteins’ evolution under the influence of their abundances and genomic GC content

Sci Rep
PMCID: 5943316
PMID: 29743515
DOI: 10.1038/s41598-018-25364-1
call_split See protocol

[…] ces based on their original sequences. Numbers of substitutions per nonsynonymous site (Ka) and numbers of substitutions per synonymous site (Ks) were calculated following Yang’s definition using the PAML package, with default parameters. […]


Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species

BMC Genomics
PMCID: 5944053
PMID: 29743014
DOI: 10.1186/s12864-018-4744-4

[…] n substitution models. Based on reported methods [, ], to find evolutionary traces of selective pressures, we analysed each group to infer ω (the ratio of nonsynonymous to synonymous distances) using Codeml implemented from PAML4.9 [, ]. We employed a complete deletion method when analysing alignments with gaps, and eliminated sequences that contained 40% of their length or more as InDels. We dete […]


Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution

BMC Genomics
PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] -copy orthologous groups in which the gene tree topology after the TreeFix analysis was identical to the species tree topology (i.e. gene trees in which the sequences appear to be orthologs). We used PAML v. 4.8a [] to test whether any of these single-copy orthologous groups exhibited shifts in gene-wide dN/dS [] and to test for episodic positive selection acting on a proportion of sites []. For b […]


Reconstruction of a replication competent ancestral murine endogenous retrovirus L

PMCID: 5930517
PMID: 29716624
DOI: 10.1186/s12977-018-0416-3

[…] pology (-m GTRCAT -# 1000 -x 13 -k -f a). Thereafter, the tree was midpoint rooted. The MSA together with the phylogenetic tree were used to guide an ML ancestral reconstruction using baseml from the PAML package [] (model: REV, initial values of alpha and kappa were calculated on the MSA by jmodeltest [], branch lengths were used as initial values). For the ancestral reconstruction of the gag ORF […]


Whole genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044

[…] To determine the genes that underwent positive natural selection in the Mikado pheasant, CODEML from PAML (PAML, RRID:SCR_014932), version 4.8 [], was applied to the branch-site model to investigate the genes in positively selected sites of the Mikado pheasant. For the branch-site model, […]


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PAML institution(s)
Department of Biology, Galton Laboratory, University College London, London, UK
PAML funding source(s)
Development of the software has been supported by grants from the Biotechnological and Biological Sciences Research Council (BBSRC) and the Natural Environment Research Councils (NERC).

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