T-Coffee

[…] uaft2 np_196684.1, at5g11230; at uaft3 np_194965.1, at4g32390; at uaft4 np_180122.1, at2g25520), as well as other cryptococcal (cn) nsts., sequence alignment between uxt1 and uxt2 was analyzed using t-coffee (http://tcoffee.crg.cat/apps/tcoffee/do:regular) and formatted using boxshade (http://www.ch.embnet.org/software/box_form.html). the protein sequences were analyzed for predicted […]

[…] conserved among 11 geobacillus and 7 parageobacillus genomes, including the 3 genomes sequenced in this study. a total of 1,355 conserved proteins were identified using orthofinder 15, aligned using t-coffee 16, concatenated and trimmed using gblocks 17 before the resulting alignment (296,082 amino acids in length) was used to construct a core genome maximum likelihood phylogeny using phyml-sms […]

[…] sequences with the characteristic domains of the family were used to perform phylogenetic and other comparative analyses. the protein sequences were multiply aligned using the accurate mode of t-coffee (57). this method takes into account the 3d structures available for improving the alignment quality. prottest v3.2.2 (58) was applied to find an optimal substitution model […]

[…] 11 species. for the analysis, we used orthomcl (v2.0.9; li et al. 2003) to identify 1:1 orthologs by clustering the sequences by similarity and then generated an msa (for each ortholog group) with t-coffee v11.00 (mcoffe mode; notredame et al. 2000). after filtering the msas with trimal v1.4 (-automated1 option; capella-gutiérrez et al. 2009), we estimated the best-fit amino acid substitution […]

[…] between positions 10 and 32 and between 320 and 342 (fig. s1)., multiple sequence alignment of mrh1 in comparison to active and inactive protein kinases from arabidopsis thaliana was performed with t-coffee83 and examined using jalview84. sequence logos were produced using weblogo3.485. a structural model of mhr1’s putative kinase domain was created with the i-tasser server86. i-tasser first […]