Tag: codeml

Abstract Cotinus is an oligo‐specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy of Cotinus was mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced…

Kopp, A. Dmrt genes in the development and evolution of sexual dimorphism. Trends Genet. 28, 175–184 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Zarkower, D. DMRT genes in vertebrate gametogenesis. Curr. Top. Dev. Biol. 102, 327–356 (2013). Article  CAS  PubMed  Google Scholar  Zhang, T. & Zarkower, D. DMRT proteins…

Q. BioPython: CodeML FileNotFoundError: [WinError 2] 0 I’m trying to run codeml in Biopython, following by Biopython cookbook. But it doesn’t work with an FileNotFoundError: [WinError 2]. I found ctl file does not contain file’s full path, like seqfile = seq2.phy outfile = result.out treefile = template.tree Files are on…

How do I compare evolutionary estimates between two sequence groups in codeML? 0 I understand that my end result will be a LRT statistic for me to ponder, and I understand that I need to use a branch model. However, I currently don’t know how to partition my sequence groups…

Testing Evolutionary Hypothesis ( branch-sites ) 0 Hy community! I am testing Evolutionary Hypothesis, I have tried two model bsA (positive-selection / branch-site) and bsA1 (relaxation / branch-site) and I get exactly the same log-likelihood value. What could it means? It is something that happens often when comparing different models?…

Translation table for annotating fish genomes ? 1 Hi, I heard there was 3 good annotation pipelines for genome annotation. 1) Maker – Need access to rep base (proprietary) 2) Braker – open source 3) Augustus – open source According to the manual Braker pipeline only uses translation_table = 1…

How codeml detects positive selection 0 Hi, I am using the codeml package of the PAML software for positive selection analysis. I have tried to read the manual as well as the other literature of the software but still I have a question about how it actually detects the positive…

Codeml giving different chi2 values when reducing the number of sequences 0 Hi, I am using codeml for my positive selection analysis. I have 93 E. coli sequences for my analysis. I run the analysis using the 93 sequences against NSsites model 1 and 2 and the corresponding chi2 value…