Sentence examples for two concatenated alignments from inspiring English sources

is the constrained structure on the first (second resp). of the two concatenated alignments.

We began analysis of the Melainabacteria genomes by constructing phylogenetic trees based on two concatenated alignments of broadly conserved single copy marker genes (see Materials and Methods; supplementary table S2, Supplementary Material online, and Darling et al. [2014]).

We concatenated all the disease-associated genes and all the other genes (for which SNP data was available) separately, and all the sites containing any missing data or indels were excluded from the two concatenated alignments.

We further calculated the Ka/Ks ratio for each branch for a concatenated alignment of all 6,324 orthologs and 1,000 concatenated alignments constructed from ten randomly chosen orthologs, and found that both data sets exhibited a significantly higher Ka/Ks ratio for the G. pachycheilus branch than other fish branches (Wilcoxon rank sum test, P < 2.2 × 10−) (fig. 2 C and D).

To estimate lineage-specific evolutionary rates for each branch of the five species, the Codeml program in the PAML package (Yang 2007) with the free-ratio model (model = 1) was run on each ortholog, a concatenation of all alignments of the orthologs, and 1,000 concatenated alignments constructed from ten randomly chosen orthologs.

We integrated the phylogenetic reconstruction of Prochlorococcus from gene order data as well as concatenated alignments, and proposed two alternative phylogenies of the genus Prochlorococcus in Figures 3A and 3B.

The analyses of ago-1 were done separately for each of the three regions as well as for concatenated alignments.

In another study, although concatenated alignments indicated a robust tree for the Alphaproteobacteria, no two phylogenies obtained from individual families were alike [ 12].

We concatenated alignments of 3,089 single-copy genes shared by at least ten species and reconstructed a fully resolved and well-supported maximum-likelihood phylogeny.

Moreover, when estimated by (4) from the eight considered character supermatrices, η varies from 52 (concatenated initial multiple sequence alignments) to 60 (concatenated alignments trimmed by Noisy).

For the BI analyses, we analyzed a partitioned (according to the above established parts) concatenated alignment of all five nuclear regions using MrBayes 3.1.2 [ 65, 66] at the Bioportal.