Selected article for: "ML likelihood and substitution model"
Author: Kamau, Everlyn; Oketch, John W.; de Laurent, Zaydah R.; Phan, My V. T.; Agoti, Charles N.; Nokes, D. James; Cotten, Matthew
Title: Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia
  • Document date: 2020_1_2
    • ID: 1qgpa45q_33
    Snippet: A dataset of HMPV genome sequences was retrieved from ViPR in order to infer relationship between HMPV viruses from Kenya and Zambia and viral populations sampled globally. The dataset included 138 sequence entries (> 13,000 nt) that included date (year) and location of sample Table S3 ). Sequence alignment was done using MAFFT v.7.221 [32] using the parameters 'localpair -maxiterate 1000'. IQ-TREE was used to infer maximum likelihood (ML) trees .....
    Document: A dataset of HMPV genome sequences was retrieved from ViPR in order to infer relationship between HMPV viruses from Kenya and Zambia and viral populations sampled globally. The dataset included 138 sequence entries (> 13,000 nt) that included date (year) and location of sample Table S3 ). Sequence alignment was done using MAFFT v.7.221 [32] using the parameters 'localpair -maxiterate 1000'. IQ-TREE was used to infer maximum likelihood (ML) trees of the complete genome and individual genes under general time-reversible (GTR) substitution model with gamma-distributed among-site rate heterogeneity. A summary of the methodology outlined here is depicted in Fig. 5 .

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